5 ms·

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

74 points by curtis 7y ago

bsaul 7y ago
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.
- edflsafoiewq 7y ago
  Man is a featherless biped having broad nails.
- phyzome 7y ago
  Inheritance is still a thing. It's just that there are occasional mix-ins. Or something like that. :-)
  - deleted 7y ago
    [deleted]
- vikramkr 7y ago
  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.
- goatlover 7y ago
  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.
  - chousuke 7y ago
    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?
    - PaulHoule 7y ago
      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.
      - chousuke 7y ago
        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.
        tempguy9999 7y ago
        > 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.
- dexen 7y ago
  >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.
- dwaltrip 7y ago
  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.
mighty_bander 7y ago
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.
- vikramkr 7y ago
  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-who-are-our-closest-relatives/ http://sitn.hms.harvard.edu/flash/2014/origins-of-eukaryotes...
  - mighty_bander 7y ago
    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 https://www.nature.com/articles/nature21031
- madhadron 7y ago
  > 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.
  - stochastic_monk 7y ago
    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.
PaulHoule 7y ago
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.
- ianai 7y ago
  They called it part of the known unknowns in the article.
- criloz2 7y ago
  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
akkartik 7y ago
The 'scoreboard' at https://en.wikipedia.org/wiki/Eukaryote#Classification https://en.wikipedia.org/wiki/Eukaryote#Classification makes for fascinating reading.
carapace 7y ago
I have to mention this (linked from the OP) https://blogs.scientificamerican.com/artful-amoeba/surprise-discovered-inside-shaggy-shimmying-protists-video/ 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-microbes-exchange-fire-with-elaborate-subcellular-weapons-video/ https://blogs.scientificamerican.com/artful-amoeba/marine-mi... Just wow.

74 points by curtis 7y ago

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.

edflsafoiewq 7y ago
Man is a featherless biped having broad nails.
phyzome 7y ago
Inheritance is still a thing. It's just that there are occasional mix-ins. Or something like that. :-)
- deleted 7y ago
  [deleted]
vikramkr 7y ago
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.
goatlover 7y ago
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.
- chousuke 7y ago
  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?
  - PaulHoule 7y ago
    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.
    - chousuke 7y ago
      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.
      - tempguy9999 7y ago
        > 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.
dexen 7y ago
>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.
dwaltrip 7y ago
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.

mighty_bander 7y ago

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.

vikramkr 7y ago
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-who-are-our-closest-relatives/ http://sitn.hms.harvard.edu/flash/2014/origins-of-eukaryotes...
- mighty_bander 7y ago
  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 https://www.nature.com/articles/nature21031
madhadron 7y ago
> 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.
- stochastic_monk 7y ago
  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.

PaulHoule 7y ago

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.

ianai 7y ago
They called it part of the known unknowns in the article.
criloz2 7y ago
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

akkartik 7y ago

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

carapace 7y ago

I have to mention this (linked from the OP) https://blogs.scientificamerican.com/artful-amoeba/surprise-discovered-inside-shaggy-shimmying-protists-video/ 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-microbes-exchange-fire-with-elaborate-subcellular-weapons-video/ https://blogs.scientificamerican.com/artful-amoeba/marine-mi... Just wow.