Tiny fern has the largest genome of any organism on Earth | Hacker News Reader

Tiny fern has the largest genome of any organism on Earth

phys.org

205 pointsPaulHoule126 comments

Many plants have huge genomes. Maybe they didn't evolve macros or subroutines or something. Anyone know anything about this?

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.

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.

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.

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...

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.

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.

Article doesn't mention ploidy, source paper says octoploid.

Maybe it's recursively encoding JSON as JSON strings many levels deep, and it's mostly backslashes and double quotes.

To be concise: Its DNA is mostly just copies. A lot of plants do this.

Recursively escaped JSON is anything but concise, because it's not simply copied, but also backslashes are exponentially doubled at each level of recursion.

  s = {"foo": "bar"}
  for (let i = 0; i < 10; i++) s = JSON.stringify(s);
  s

"\"\\\"\\\\\\\"\\\\\\\\\\\\\\\"\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\"\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\"\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\"\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\"\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\"{\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\"foo\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\":\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\"bar\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\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  for (let i = 0; i < 10; i++) s = JSON.parse(s);
  s
  {"foo": "bar"}

Plants ain't got brains. Gotta use their genome to process information.

/Wild speculation.

Long term strategy

Plants were the OG LLMs.

This 160 Gbp genome dwarfs the human genome by over 50 times. Yet, its complexity as an organism doesn't match this genomic enormity. This stark disconnection, a modern twist on the C-value paradox, suggests that genome size and organism complexity are far from straightforwardly linked. Instead of functional genes, the vast expanse of DNA is dominated by polyploidy and non-coding repetitive elements. This discovery pushes us to rethink the biological and evolutionary implications of such massive genomes and what drives their expansion.

It’s like with programming. A junior dev writes 50 lines of code for what I can solve in 5 loc.

Maybe it’s the long term data storage tech used by a prior civilization?

Or just added redundancy for radiation resistance. There was less oxygen and subsequently less ozone when ferns first evolved, so there would be far more UV light to protect against.

No, that's bamboo: https://scp-wiki.wikidot.com/scp-2528

At least they should have mentioned:

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

"we don't know what it does, therefore is is junk" feels like a very arrogant and/or short sighted way of thinking to me.

"We don't know what it does, but junk DNA is a real thing, and that's one possible explanation" is a lot more reasonable. And I think that's a more charitable reading of the comment you replied to.

As you'll often hear from geneticists these days, one person's junk is another person's treasure.

There certainly was an attitude for a long period of time that our DNA was full of junk[0], but the field has since characterized much of what we once thought was junk (i.e. non-functional DNA) actually is just non-coding DNA[1] that serves one or more of a wide array of biological functions.

In many ways, you can't really blame scientists of the 70s for thinking that much of what we now know is ncDNA was inscrutable junk. In many ways, given the technology at the time, it was.

It's a super interesting area of study.

[0] https://pubmed.ncbi.nlm.nih.gov/5065367

[1] https://en.wikipedia.org/wiki/Non-coding_DNA

> junk (i.e. non-functional DNA)

Perhaps people should use the term "non-functional DNA" instead of "junk DNA" more often. Calling something as "junk" has unnecessarily dismissive connotations.

They should call it non-translating-to-protein-but-probably-has-some-function DNA

Even non-functional isn't nearly as good as "genetic data with unknown function or expression".

Non-coding DNA (ncDNA) seems good to me. (https://en.wikipedia.org/wiki/Non-coding_DNA)

That's a very different concept. There's a lot of non-coding DNA that has never been considered non-functional/junk.

Or UCO... unidentified coding object.

I don't know. The concept of junk DNA never made sense to me because, besides proteins, you need to know how to assemble everything and when.

The idea behind junk DNA was that the rest of it didn't code for proteins and therefore was junk.

But if I give you a list of parts for a Boeing 747 that's not enough information to build the jet.

I never understood how this was not obvious to scientists.

I still remember being taught the concept of junk DNA in high school, and didn't believe it then.

Junk DNA can also affect spatial organization of the genome, thereby affecting its usage.

Still 90% junk.

https://sandwalk.blogspot.com/2011/05/whats-in-your-genome.h...

65% junk according to the link, which is over a decade old.

They're not calling it junk as part of an effort to down play it or to cause the rest of the field to deprecate or ignore it.

They're calling it that because the result is baffling. It's meant to be a call to action, not an affront to reason.

"Mystery DNA", or "enigmatic basepairs" might have conveyed a call to action. "Junk" definitely has a dismissive vibe to it.

How about "uncharted" or "here be dragons" (https://en.wikipedia.org/wiki/Here_be_dragons) DNA?

"Junk DNA" was a terrible name. But the article really should have mentioned something about how much of it actually codes for proteins (for both the fern and us).

Has there been experiments about trimming down its DNA to find a ‘Minimum Reproductive Fern’?

Hmm, I’ll need to check but the genome of the single cell protozoan, Polychaos dubium, was reported in 2004 to have a genome of 670 billion basepairs. Perhaps this was an error.

Weren't the first plants on land ferns or fern-like?

The first land plants were likely similar to mosses or liverworts.

I can imagine an alien species storing information in plants. It’s like a self replicating database.

I instead think of nature as storing information in living organisms. It is indeed a self replicating database that is forever optimising ways to improve the replication.

How do they know it's the largest? They should rather say it's the largest known if anything.

I think that is pedantic and goes without saying. There are always unknown unknowns.

Yes and no. Scientists throw out these sorts of terms and know what they mean but the general population doesn't and doesn't get the ramifications of the real meaning. Just see how many people think that when a scientist says "the universe" that they mean the entire universe and not, as scientists mean, the observable universe. For general, "pop" cosmology those have very different meanings and lead to all sorts of bad thinking.

> Just see how many people think that when a scientist says "the universe" that they mean the entire universe and not, as scientists mean, the observable universe

We once pestered our physics professor to explain what’s outside the universe. He finally said that’s a dumb question, the universe is definitionally everything, if we find anything beyond the edge of the universe, we’ll just call that universe too.

Always liked that framing.

In many contexts, "the universe" means "the whole universe [to the best of our knowledge]". For example, when scientists talk about the age of the universe or the start of the universe or the ultimate fate of the universe, they really do mean the whole universe, not just the observable universe.

So sometimes scientists are just talking out of their ass. They are people after all, so it should be expected sometimes.

Not really, the observable universe is a specific part of the universe we know of. We also know a lot of things about the parts of the universe outside the observable universe. In time, some parts of what is today the observable universe will become unobservable (since they are receding at an accelerating speed because of dark energy). That doesn't mean they will cease to be things we talk about when we say "the universe".

Now, is it possible that some day we'll see new stars or something else coming from a completely unexpected direction, and discover that the universe also contains things that did not begin at the big bang? Sure, it's always possible, and our theories will change. But it's absurd to qualify each statement based on the possibility that new knowledge will come along at some point, when the same qualification always applies.

Observation is a cornerstone of science and theorizing about something you cannot observe is interesting but not science. This is speculation about what might be outside the observable universe and that could lead to science disproving those particular speculations, but speculation is not science, it is philosophy.

Observation is not limited to direct observation. You can take what you're seeing with instruments, and extrapolate based on known laws, and you're still doing science. In fact, this is even more important to science than direct observation, which is extremely limited. By direct observation, I can't even tell if the earth was here yesterday, or at least a thousand years ago, even less so if it will still be here tomorrow.

By the same token, when you look at certain characteristics of what you can observe of the universe, and you take the known laws of physics, you can find out a lot about the unobserved, and the un observable, universe.

When Carl Sagan said "Ten Bill Yun Bill Yun Bill Yun Atoms", he actually meant "Ten Billion Billion Billion Atoms".

https://www.youtube.com/watch?v=HbkzNkskRTs

He explained what came after the Big Bang, and where the term UFO came from:

https://www.youtube.com/watch?v=iIbbTHQmPkE

And when he said "BEEP. BEEP BEEP. BEEP BEEP BEEP. BEEP BEEP BEEP BEEP BEEP." he really meant "1. 2. 3. 5."

https://www.youtube.com/watch?v=cPM5WpS65tk&t=470s

Which could be a sign of ET communication:

https://www.youtube.com/watch?v=TFflESQCRsI

While I understand there are unknown unknowns, in science you can sometimes prove that something cannot be smaller or something cannot be bigger. Because it would simply not be possible. Not sure if that's the case for DNA.

And I am not talking about unknown unknown like some living organism using some other "substance" as the generic material.

What share of the total organism weight would be the DNA? Is it something non trivial in this case?

I can't imagine its very much, probably still mostly water and structural polysaccharides.

No explanation of why this tiny fern has such a huge genome?

Because it somehow survived millions of years despite that massive inefficiency holding it back. Quite remarkable luck not getting out-competed to extinction.

> despite that massive inefficiency holding it back

I assume you are referring to the size of the genome. Has anyone been able to prove that it is causing an inefficiency? Maybe it isn't. In classical computer programming languages sometimes more code is more efficient, such as unrolled loops. That analogy may not apply here. I am far from knowledgeable in this realm.

If it's really just inefficiency, wouldn't a mutation that removes some of the surplus genome bring an evolutionary advantage? Those mutations are probably rare and the advantage miniscule, but anything adds up over a long enough timeframe

Not ferns specifically, but I've read a simplistic explanation that plants lack behavioral defenses, so they rely on chemical defenses. And more chemical defenses requires more genes.

Cats have longer genomes than dogs too FYI.

So bloat-ware ?

It'd be a hell of a job to demonstrate that all that information couldn't be useful in the right environment, very much unlike bloatware.

sounds exactly like bloatware. it was designed for something, it just doesn’t happen very often

is it a memory leak?

memory leek?

Might be relevant and interesting:

https://www.thenewatlantis.com/publications/getting-over-the...

No garbage collector in nature ?

Clunky code. Slow growing. Makes sense.

Imagine a whole different plant hidden in a species but never expressed.

Adaptability for climate change

My man Anton made a video about it

https://invidious.private.coffee/watch?v=QhEfAHNREmM

Awful summary video, in my opinion. Takes 5 minutes to get to the new discovery, then spends 3 minutes repeatedly claiming that we don’t have any explanations for the wide range of genome sizes, then 2 mins of Patreon credits to get over the 10 minute mark. There might be 30 seconds of actual content in this video.

I’d give a highschooler a bad grad on this, why do so many people give this guy money to make low quality content like this?

He could have just picked any section of this Wikipedia page and read it verbatim and he would have transmitted more information: https://en.m.wikipedia.org/wiki/Genome_size

I found that video pretty interesting.

Bad channels which’ve accumulated views and subscribers getting recommended by the youtube algorithm. Hence why he has a filler segment to get the video to 10 minutes. That’s just how youtube works nowadays.

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