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Archaea: The 'Dark Matter' of the Microbial World

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Re: Archaea: The 'Dark Matter' of the Microbial World

#21

Post by jballanc »

jessriedel wrote: post #3

Is it known why there are no evolutionary intermediates between archea and eubacteria? Nick Lane's book The Vital Questions has been highly recommended by the HN commentariat, and I think it more or less deserves its esteem. Lane gives an extensive theoretical analysis of the sequence of events wherein a eubacterium was engulfed by an archea, and the resulting endosymbiosis that was the beginning of complex (eukaryot…

Archaea and Eubacteria have different Ribosomes. In the world of biology, if DNA is the source code then ribosomes are the compiler.

In other words, while both families use DNA to store information and RNA to translate it, all the rest of the machinery used by cells in that process is different. This is why there are no intermediates. Likely (and this is a guess, if an educated one) this split happened before cells were even "cells". That is, whatever the pre-cellular replicons were that eventually led to life, there might have been many variations on (what eventually became) the ribosome, but two won out and gave rise to two distinct lineages of cellular life.

The rest, as they say, is history...

Re: Archaea: The 'Dark Matter' of the Microbial World

#22

Post by throwaway2048 »

obastani wrote: post #19
mmustapic wrote: post #10

Earlier quoted context omitted.

It didn't happen like that. Humans didn't branch from chimpanzees or the other way around. At some point there was a common ancestor of both species. Its offsprings diverged into two species that continued evolving into the current humans and chimpanzees.

This doesn't really answer the question -- how come there are usually only a few clearly defined species that descended from this common ancestor? Why isn't there a spectrum? I don't know anything about the phylogenetic tree of humans and our cousins, but I assume that at some point there was a spectrum (e.g., Neanderthals), but at some point the others got wiped out, without humans splitting any further. Perhaps thi…

The most intense form of competition is that from your own species, nothing else requires exactly the same conditions/ecological niches/resources. The less fit individuals are out competed (dont breed, or die), and the species as a whole is "pulled" in a certain fitness direction that is more optimal.

The reason speciation arises is complex, but its often due to different subgroups of a species exploiting different niches, and thus experiencing differing fitness pulls that eventually give rise to new species.

There are no "intermediate" species because they fit more poorly into either niche occupied by the two other species, and thus are out competed or dont arise in the first place.

Re: Archaea: The 'Dark Matter' of the Microbial World

#23

Post by throwaway91111 »

jballanc wrote: post #21
jessriedel wrote: post #3

Is it known why there are no evolutionary intermediates between archea and eubacteria? Nick Lane's book The Vital Questions has been highly recommended by the HN commentariat, and I think it more or less deserves its esteem. Lane gives an extensive theoretical analysis of the sequence of events wherein a eubacterium was engulfed by an archea, and the resulting endosymbiosis that was the beginning of complex (eukaryot…

Archaea and Eubacteria have different Ribosomes. In the world of biology, if DNA is the source code then ribosomes are the compiler. In other words, while both families use DNA to store information and RNA to translate it, all the rest of the machinery used by cells in that process is different. This is why there are no intermediates. Likely (and this is a guess, if an educated one) this split happened before cells w…

So, if I'm understanding correctly, these pre-cellular replicons are distinctly less efficient at survival than both archaea and eubacteria, hence their not existing in any (recognizable) form today. Is this correct?

This opposed to the idea that the archaea existed, then the bridge (which went extinct), then archaea.

Re: Archaea: The 'Dark Matter' of the Microbial World

#24

Post by ihartley »

pygy_ wrote: post #6
jlarocco wrote: post #4

Earlier quoted context omitted.

That's something I've always wondered about evolution in general. Why isn't there a continuum of species? For example, why are there chimpanzees and humans walking around as discrete species with nothing "in between". Seems unlikely that a few chimpanzees gave birth to human babies (or I guess some ancient human ancestor) one day, and then we just branched off and evolved separately leaving the rest of the chimpanzee…

In general, geographic separation leads to speciation. It can be rivers (IIRC for example bonobos and chimpanzees live on different sides of the Congo river). Another interesting example is I think seagulls along the arctic circle that are split in many species spread along an east-west axis. Most species can interbreed with their immediate neighbour, but not the neighbour of their neighbour (except at one point wher…

If anyone else is curious, this is called a ring species, and there are only four known examples: https://en.wikipedia.org/wiki/Ring_species

Re: Archaea: The 'Dark Matter' of the Microbial World

#25

Post by jballanc »

throwaway91111 wrote: post #23
jballanc wrote: post #21

Earlier quoted context omitted.

Archaea and Eubacteria have different Ribosomes. In the world of biology, if DNA is the source code then ribosomes are the compiler. In other words, while both families use DNA to store information and RNA to translate it, all the rest of the machinery used by cells in that process is different. This is why there are no intermediates. Likely (and this is a guess, if an educated one) this split happened before cells w…

So, if I'm understanding correctly, these pre-cellular replicons are distinctly less efficient at survival than both archaea and eubacteria, hence their not existing in any (recognizable) form today. Is this correct? This opposed to the idea that the archaea existed, then the bridge (which went extinct), then archaea.

That is an excellent question!

I should start by saying that we don't know, for sure, that pre-cellular replicons don't still exist. They may, and we may just not have figured out the right place to look for them.

That said, gaining a membrane is a huge advantage for life. The current working hypothesis is that life started as a series of autocatalytic chemical reactions, but for this to work there must have been just the right combination of chemicals in just the right conditions all at the same time. You can imagine that it wouldn't take much of a stray current to wash all that away, and you're back to square one. By surrounding themselves with a membrane, pre-cellular replicons could begin controlling their chemical environment, enriching it with the raw materials needed and regulating the conditions.

Again, though, just because cellular life would be expected to be more robust and, therefore, more successful than acellular replicons, you wouldn't expect those acellular reactions to immediately halt once cellular life arose.

If I had to guess, I'd say that acellular replicons may have persisted for quite some time, but ultimately succumbed to the Great Oxygenation Event (https://en.wikipedia.org/wiki/Great_Oxygenation_Event). Shortly after cellular life arose (or possibly beginning a bit before cells came on the scene), life cause a massive shift in the Earth's chemistry, freeing vast quantities of oxygen and changing what had been a reducing environment to one that is, on the balance, oxygenating.

Oxygen is, to put it bluntly, nasty stuff. It tends to break down complex molecules very readily, and so any acellular replicons that may have survived up to the Great Oxygenation Event were likely wiped out soon after.

Re: Archaea: The 'Dark Matter' of the Microbial World

#26

Post by delhanty »

ihartley wrote: post #24
pygy_ wrote: post #6

Earlier quoted context omitted.

In general, geographic separation leads to speciation. It can be rivers (IIRC for example bonobos and chimpanzees live on different sides of the Congo river). Another interesting example is I think seagulls along the arctic circle that are split in many species spread along an east-west axis. Most species can interbreed with their immediate neighbour, but not the neighbour of their neighbour (except at one point wher…

If anyone else is curious, this is called a ring species, and there are only four known examples: https://en.wikipedia.org/wiki/Ring_species

>non-breeding, though genetically connected, "end" populations may co-exist in the same region

This reminds me of the Riemann surface associated with the complex logarithm:

https://en.wikipedia.org/wiki/Complex_logarithm#The_associat...

Re: Archaea: The 'Dark Matter' of the Microbial World

#29

Post by patall »

jessriedel wrote: post #20
dekhn wrote: post #5

Earlier quoted context omitted.

Lane has a good story and tells it nicely, but I don't think he represents the mainstream, and he conveniently throws all the evidence that doesn't agree with him under the rug.

Thanks. I did get that impression. Is even the basic eubacteria-inside-archea claim is disputed?

Depends on how specific you are as endosymbiotic theory can be very complicated. For example, the nucleus itself could be regarded as a seperate cell itself (which would be the archea), but what was the sourding cell?

Re: Archaea: The 'Dark Matter' of the Microbial World

#30

Post by zeroer »

jlarocco wrote: post #4
jessriedel wrote: post #3

Is it known why there are no evolutionary intermediates between archea and eubacteria? Nick Lane's book The Vital Questions has been highly recommended by the HN commentariat, and I think it more or less deserves its esteem. Lane gives an extensive theoretical analysis of the sequence of events wherein a eubacterium was engulfed by an archea, and the resulting endosymbiosis that was the beginning of complex (eukaryot…

That's something I've always wondered about evolution in general. Why isn't there a continuum of species? For example, why are there chimpanzees and humans walking around as discrete species with nothing "in between". Seems unlikely that a few chimpanzees gave birth to human babies (or I guess some ancient human ancestor) one day, and then we just branched off and evolved separately leaving the rest of the chimpanzee…

There is a continuum of species, but they don't exist at the same time.

Take a human woman. She holds hands with her mother. Her mother holds hands with her mother, and so on.

Take a female chimpanzee. She holds hands with her mother. Her mother holds hands with her mother, and so on.

Eventually, these two chains meet the same organism, the last common ancestor of human and chimpanzee, who lived somewhere around 6 million years ago. This (now singular) chain has somewhere around 600,000 individual organisms, where each pair next to each other holding hands are related as mother-daughter (so how could you argue they're different species?), but the endpoints of the chain are modern human and modern chimpanzee.

As a side note, categorizing life via the idea of species seemed like a good idea when it was developed, but we now know it's not. There's other (real life) examples that show that the idea of species is just a human invention that humans try to fit onto a reality that's more complicated and doesn't respect human abstractions.

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