What a Newfound Kingdom Means for the Tree of Life (2018) | Hacker News Reader

What a Newfound Kingdom Means for the Tree of Life (2018)

scientificamerican.com

74 pointscurtis27 comments

Wonder if biology is going to experience the same transition from inheritance to composition that computer science went through those last two decades, and stop building trees of classes, but rather favor describing species by a composition of elementary attributes.

Man is a featherless biped having broad nails.

Inheritance is still a thing. It's just that there are occasional mix-ins. Or something like that. :-)

Biology transitioned away from the whole composition of elementary attributes thing- that's how it started and then we realised that attribute based categorization was kind of useless. The approach we have now at least categorizes things by something more biologically relevant- inheritance and evolution - both of which are core important parts of the field.

No, because the tree of life is based on common descent for the various populations going back to a single ancestor in the very distant past.

Makes me wonder, was it actually a literal "single ancestor" at any point, or are we be the result of several completely unrelated populations doing horizontal gene transfers (or whatever it would've been before actual genes were a thing)?

What little I know of what we know, it doesn't seem completely implausible to me for self-replicating molecules to have appeared multiple times on the young Earth. Is it possible for these hypothetical multiple starts to have been be chemically compatible?

There was a huge horizontal gene transfer event when us Eukaryotes were born from a train crash between the Bacteria and the Eubacteria. Thus you can't trace out a single "tree" of life all the way to the root.

I'm vaguely aware of that, but I was thinking about life even earlier. That is, instead of having a single universal common ancestor to all life that currently exists, would it have been possible to have a set of separate strands of life that arose from abiogenesis (or however it started) and later merged?

I like the thought, though I'm aware that that alone doesn't make it more likely to be true. I'm just wondering if we know something that rules out the possibility.

> to have a set of separate strands of life that arose from abiogenesis (or however it started) and later merged?

Not impossible but likely ever impossible to prove.

I have read a theory that in the earliest days before impermeable cell walls formed, all dna (or whatever it was then) was being madly swapped around because horizontal transfer couldn't be stopped. No lineage then, but an amorphous glob of all life. When life got more sophisticated it then differentiated, because it could block horizontal transfer. But again, who knows.

'Madly swapping DNA around' happens to this day at the bacterial/archaeal level.

The argument against multiple "strands" of life is simple: if abiogenesis of a single replicator is extremely improbable, abiogenesis of multiple such replicators is much less likely still. Plus, almost by definition, the first successful replicator will start replicating and eating all it can around itself, strongly altering environmental conditions and closing the doors for anything that could spontaneously arise after it.

> if abiogenesis of a single replicator is extremely improbable

If [0]

> the first successful replicator will start replicating and eating all it can around itself

Assuming such life looked much like it does now, yes. It may, it may not.

I'm not disagreeing with you, these are valid points but we can't know and I am uneasy about speculating in such a case.

[0] https://en.wikipedia.org/wiki/Laconic_phrase

After invading southern Greece and receiving the submission of other key city-states, he [Philip II of Macedon] turned his attention to Sparta and asked menacingly whether he should come as friend or foe. The reply was "Neither."

Losing patience, he sent the message:

"You are advised to submit without further delay, for if I bring my army into your land, I will destroy your farms, slay your people, and raze your city"

The Spartan ephors again replied with a single word:

"If"

If you're interested in this stuff, you should check out the book "The Vital Question" by Nick Lane. It's an absolutely fascinating exploration of this topic. Blew my mind.

Basically, as best we know now life did have a common ancestor in ancient bacteria and there was a split at some point into eukaryotic bacteria/cells leading to more complex life.

I believe "LUCA" fits the description: the last universal common ancestor from which all organisms now living on Earth have a common descent.

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

It gets somewhat screwy given that some organisms are symbiotic, eg lichen, which are composite of algaea and funghi.

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

Not really. At the very least, bacteria and archaea engage in lateral gene transfer as much as they do in reproduction, making any exercise in building a universal tree pointless.

The phylogenetic tree you may have seen is based on trying to trace inheritance of a very particular piece of molecular machinery that's unlikely to be lost and reintroduced through lateral gene transfer. There are many such pieces, and the trees drawn for each of them are completely different from each other.

Nick Lane's "The Vital Question", mentioned downthread, makes a big point about that.

>composition

I know it's not what you are asking, but... the mitochondria are example of biological composition. They are organisms that (d)evolved to live exclusively inside eukaryotic cells, in tight symbiotic relationship.

Viral genetic inserts in our genome are another kind of composition. And then there's the gut microbiome, without which we couldn't live off of the diets we do.

Nonetheless, the inheritance aspect still is, and will remain, practical and worth taking about; saying "human IS-A mammal" is valid and useful.

There may be a hint here, regarding the current trend away from inheritance.

Taxonomy used to be based purely on visible traits, and then genetic analysis came along and showed us we had made many mistakes with this approach. Of course, looking at morphology and such is still very useful, but it isn't sufficient.

Biologists have long known that most microbes are "dark matter" in the sense that we don't know how to culture them independently.

There are all sorts of strange things such as huge rod bacteria that have lots of little rod bacteria living on their surface.

Many unknown organisms make themselves visible through their DNA, but without the ability to culture them independently we can't tell which are which.

They called it part of the known unknowns in the article.

trying to interpret a fractal without context, it can be anything. dark matter is just the graph of morphisms between the identity functors of the local objects of a subregion of the space, without this graph, you will not be able to interpret those dnas

The 'scoreboard' at https://en.wikipedia.org/wiki/Eukaryote#Classification makes for fascinating reading.

I have to mention this (linked from the OP) https://blogs.scientificamerican.com/artful-amoeba/surprise-...

Not to spoil it but there's a rotating organelle(?)! (Among other things.)

And these rocket-propelled harpoons:

https://blogs.scientificamerican.com/artful-amoeba/marine-mi...

Just wow.

Archaea are interesting and often overlooked because they aren't numerous relative to bacteria. The domain Archaea always struck me as more of a "junk drawer" than a genuine grouping.

We are also likely to be a descendant of them, which makes them even more interesting IMO. We seem lot more similar to bacteria on the surface which makes it strange that we might be more closely related to archaea. And let's not forget that we are part bacteria as well - and I dont mean the microbiome. Our mitochondria are fascinating.

http://sitn.hms.harvard.edu/flash/2014/origins-of-eukaryotes...

Funny story - I read an article linked from the one in the original post, and then replied about that, having forgotten where I started. You might find it interesting.

https://www.nature.com/articles/nature21031

> Archaea always struck me as more of a "junk drawer" than a genuine grouping.

Why do you say that? They emerged from the large scale structure of 16S rRNA trees, which is what defined them as separate from bacteria.

You’re correct, the above poster is more enthusiastic than accurate. I knew Carl Woese, who discovered Archaea through this analysis, during my time at UIUC.

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