What a Newfound Kingdom Means for the Tree of Life

https://www.quantamagazine.org/what-a-newfound-kingdom-means-for-the-tree-of-life-20181211/

by dnetesn • 8 years ago

262 69 8 years ago

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.

notafraudster2• 8 years ago

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.

jdleesmiller2• 8 years ago

I would say it's accessible, yes. My background is CS and math, and I have managed to follow most of it, though I have occasionally got lost on some of the chemistry.

Radim2• 8 years ago

Bill Bryson's "A Short History of Nearly Everything" is an amazing layman start.

It's a little dated (the first edition came out in 2004!) but to be honest, if you're interested in a "human-focused" intro and how the concepts fit together, things haven't really changed that much.

matt40777• 8 years ago

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

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

iamphilrae• 8 years ago

Richard Dawkins’ The Ancestors Tale is a great layman introduction, on par with Bill Bryson’s as mentioned a few posts up. I’ve read both. Both cover similar subject matter, but approach it from opposite chronological orders.

rsync• 8 years ago

"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?"

I have not yet read _The Vital Question_ but I have read his previous books and I highly, highly recommend:

_Power, Sex, Suicide_ _Oxygen_

If I had to pick just one, it would be PSS.

reubenswartz2• 8 years ago

Only bio class I took was in high school. The Vital Question is tricky in some places (I don't pretend to understand all of the details), but accessible, interesting, and one of my favorite books of the last few years. Of course, YMMV, but don't let that hold you back.

sparkcc• 8 years ago

accessible!!

yters3• 8 years ago

Why is it still taught as a tree, then? That seems like a pretty big discrepancy to just be a matter of "simplifying". Would also be more inspiring to students to know there is so much more to discover, as you point out.

klodolph3• 8 years ago

Well, chunks of it are tree-like and chunks of it have less well-defined structure. The tree still works very well. We still teach the Bohr model of the atom, too.

matt40777• 8 years ago

Because it is a tree. Each branching point represents the last common ancestor between two species.

The only confounding factor is that among bacteria, there is a process called “horizontal gene transfer”, where one bacterium inadvertently (?) aquires some genetic information from another when they’re really just out for a quick snack. Plus viruses, which sometimes just get inserted into a host’s genome and becomes part of it, sometimes even functional. The way animals acquired mitochondria is also a fascinating divergence from the standard “tree” model, although it’s somewhat derivative of how plants acquired photosynthesis.

(That’s how everything in biology works. It’s the worst case of spaghetti coding, ever, full of self-modifying compilers, state saved in the JIT’s buffer, and programs only working by exploiting CPU flaws depending on the Hall effect, but only on workdays (according to the Julian calendar), fan speed, and your database server’s support of OpenGL).

But it’s really just a tree.

What’s far less of a “real” concept, is that of species. That makes essentially no sense in non-sexually reproducing organisms.

im3w1l• 8 years ago

Imagine if there is something really ancient out there but it's dying because of global warming or something. That possibility makes me sad.

seibelj2• 8 years ago

Over the last 1+ billion years the Earth has gone through many shocking events. Not just large changes in global temperature through ice-age and warming periods, but the atmosphere composition, asteroids, super volcanoes, and so on. If the ancient life form is still alive today after all of that, I doubt global warming would cause it to die.

DEADBEEFC0FFEE• 8 years ago

They maybe something in the soil of colder climates, desperately clinging on to existence, needing just a few degrees more heat to thrive. Either way, I find these articles about new life discoveries fascinating.

ryan-allen• 8 years ago

School should do this with other areas of science, I remember being taught about atoms and how 'absolutely true' it was that they were the smallest possible things, despite the fact it was known at the time that was not the case in other areas of research.

It would have piqued my interest much more at a young age if we were taught 'this is what we have found out... so far!'. There's still so much left to discover!

kashyapc• 8 years ago

A small digression on Nick Lane's book: I gifted myself The Vital Question in 2015 December. While Lane writes quite effectively without any mind-numbing jargon, the book still has quite a bit of technical chemistry (understandably). After the excellent first 80 pages, it took me a lot more will power to plough through. :-) (I paused at page 112 and never got back. Thanks to this reminder, I'll resume again.)

When I was reading the book on a plane, a seasoned biologist happened to be sitting next to me. When I said that it's the first book of Nick Lane that I picked up, he said: "I'd rather suggest you to pick up Laine's other book, Life Ascending, and then get back to The Vital Question."

(Edit: Oops, bad me, just noticed that there's already discussion about the book's accessibility in this thread.)

burning_hamster2• 8 years ago

pick up Laine's other book, Life Ascending, and then get back to The Vital Question

As an ex-biochemist who has read both books, this is excellent advice.

dannykwells• 8 years ago

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...

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.

ademup• 8 years ago

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.

bkohlmann• 8 years ago

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• 8 years ago

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• 8 years ago

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

https://chem.tufts.edu/answersinscience/relativityofwrong.ht...

"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."

21• 8 years ago

Science is about hypothesis, iteration, and testing

Maybe in the past. Today science is about getting grants, publishing as much as possible even if the paper is trivial or you p-hacked your way to heaven.

It's also about finding a niche where there is no competition so that you can build a name for yourself. If any sort of competition appears, quickly run away to a more fertile ground (see the recent article about DeepMind and protein folding)

zapzupnz• 8 years ago

You're talking about science, the industry. I believe the person to whom you responded is talking about science, the school subject.

jf-• 8 years ago

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• 8 years ago

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.

bloak• 8 years ago

How big is that critter?

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

astazangasta• 8 years ago

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)

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.

Jabbles• 8 years ago

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.

masonic• 8 years ago

I, for one, welcome our new hemimastigote overlords.

What a Newfound Kingdom Means for the Tree of Life

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