
What a Newfound Kingdom Means for the Tree of Life - dnetesn
https://www.quantamagazine.org/what-a-newfound-kingdom-means-for-the-tree-of-life-20181211/
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jdleesmiller
I'm currently reading Nick Lane's excellent book, The Vital Question, which
explores what we know about the split between archaea and eukaryotes, so this
was an exciting article. This discovery is still one level below that split,
within the eukaryotes, but the ongoing discoveries of more and more ancient
branches suggests the tantalising possibility that we may one day find
something even more ancient still swimming around somewhere --- a missing link
from billions of years ago.

What strikes me about both this article and Nick Lane's book is that when I
was in school the tree of life was presented as this thing that people had
pretty much figured out. Since then it's been altered almost beyond
recognition using genomics. I hope there are people still in school who read
articles like this one and get inspired to get into this amazing area of
research.

~~~
notafraudster
If I know nothing beyond high school biology about taxonomy and nothing beyond
a reasonably educated layperson about biology generally, is "The Vital
Question" accessible? If not, do you have an example of a well written but
quick introduction to the subject matter.

I occasionally read pop-culture articles about, e.g. the discovery of giraffe
subspecies, and think about how I'd like to know more about both the human-
focused taxonomy side and the evo bio speciation side, but I don't know where
to start.

~~~
matt4077
If you have a background in IT, and are modestly comfortable with statistics,
the following foundational paper on algorithms to reconstruct the tree of life
from genetic data should actually be understandable:
[http://science.sciencemag.org/content/311/5765/1283](http://science.sciencemag.org/content/311/5765/1283)

The statistics really only ever amount to Occam’s Razor, I. e. fewer
differences in the genome means closer relationship.

Edit: actually free full-text link:
[http://bioinformatics.bio.uu.nl/pdf/Ciccarelli.s06-311.pdf](http://bioinformatics.bio.uu.nl/pdf/Ciccarelli.s06-311.pdf)

~~~
notafraudster
I am a statistician (although as I confessed nowhere near computational
biology), so, uh, yeah this is up my alley.

~~~
matt4077
One more thing: Jared Diamond (of “Guns, Germs, Steel” fame) transferred the
exact, same method to linguistics, using it to discover the ancestry of
Pacific Islanders using features of their respective languages instead of
letters of DNA. The result is both a tree of their (cultural) ancestry, and a
map of their migration/expansion from island to island.

~~~
xaedes
Yet another thing: Julien d’Huy uses these methods to analyze folk literature
and myths. Very, very interesting research.

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bkohlmann
This is what excites me about science - the discovery of the previously
unknown and the revision of what we previously thought we knew.

I wish our education system promoted this idea - "what we know about science
will change in your life time. It's likely that in the future, most of what
you're learning today will be outdated. It doesn't mean what we're teaching
you is 'wrong,' but rather, it's the best of what we know now. You're about to
enter on a glorious adventure of discovery that will not end at graduation.
Science is about hypothesis, iteration, and testing...and the discovery of
unanticipated results."

Instead, what's taught is a static version of reality: What we know today is
all that is worth knowing for the rest of your life.

~~~
noonespecial
In that regard I always admired Eliezer Yudkowsky's idea of working to become
"less wrong" as you progress. It kind of sums that up perfectly.

We haven't got it all figured out yet, but we're less wrong than we used to
be.

~~~
mrob
Or before Yudkowsky, Asimov's idea of "the relativity of wrong":

[https://chem.tufts.edu/answersinscience/relativityofwrong.ht...](https://chem.tufts.edu/answersinscience/relativityofwrong.htm)

"Naturally, the theories we now have might be considered wrong in the
simplistic sense of my English Lit correspondent, but in a much truer and
subtler sense, they need only be considered incomplete."

~~~
saadat
That link omits some parts of the essay. Complete version here:
[http://hermiene.net/essays-
trans/relativity_of_wrong.html](http://hermiene.net/essays-
trans/relativity_of_wrong.html)

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dannykwells
For people interested in this kind of work, I recommend The Tangled Tree, the
biography of Carl Woese, who discovered Archaea:
[https://www.nytimes.com/2018/08/13/books/review/david-
quamme...](https://www.nytimes.com/2018/08/13/books/review/david-quammen-
tangled-tree.html)

Evolution is interesting but up and down from this level of the tree of life
too. I also loved reading "The Beak of the Finch" to learn about evolution in
macroscopic metazoans.

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astazangasta
For those interested in going deep on this, I highly recommend this essay I
was fond of in grad school by W. Ford Doolittle, who writes a lot on this
subject: [Pattern pluralism and the Tree of Life
hypothesis]([[https://www.pnas.org/content/104/7/2043](https://www.pnas.org/content/104/7/2043))

For a while now amongst evolutionary biologists it has been clear that the
"root" of the evolutionary tree, or the so-called "LUCA" (last universal
common ancestor) may not exist, mostly because horizontal gene transfer is so
common amongst unicellular lifeforms that it ruins the orderly notions of
descent-with-modification that we have formed following Darwin's studies of
higher life.

I imagine this is disheartening to most people, and the orderly notion of a
"tree of life" with a simple root persists because we want an uncomplicated
picture of the world; human needs for ontological clarity trump the disgusting
ball of muck and sputum that is actual life.

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ademup
It seems completely obvious to me that we continue to find new types of life.
Given that "More than eighty percent of our ocean is unmapped, unobserved, and
unexplored". I could not find a number that represents unexplored mud and
muck, where this specimen was found. My guess is something very close to 100.

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bloak
How big is that critter?

Answer my own question: other articles suggest it is about 15 μm long.

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Jabbles
I wonder if we will discover that this tree is "hairy" \- that there are
thousands of isolated branches that departed from the main branch hundreds of
millions of years ago. They wouldn't be "kingdoms", since they'd only contain
a few (or even one) species.

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jf-
It may be genetically distinct from animalia, but it’s definitely acting like
an animal. It moves independently, senses external stimuli and hunts prey.

Actually, it’s probably the closest thing to an actual alien life form that
we’ve yet encountered. This is what that kind of convergent evolution would
look like.

~~~
TomMckenny
As it turns out, not quite a guy with pointed ears wishing us long life and
prosperity.

Humor aside, it is a very interesting idea to find convergent evolution far
away on the tree of life to conjecture about exobiology.

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masonic
I, for one, welcome our new hemimastigote overlords.

