John Carlos Baez

Who are we all descended from? And I mean π‘Žπ‘™π‘™ - people, birds, plants, bacteria, archaea....

It's called π—Ÿπ—¨π—–π—”: the last universal common ancestor. And people have been trying to track it down. By comparing the genomes of different organisms you can infer a tree of life and guess where it leads back to.

This new paper suggests that LUCA lived about 4.2 billion years ago, with a genome having about 2.5 million base pairs.

They guess it was a prokaryote: a single-celled organism with no nucleus. They guess it was anaerobic. Neither of those are at all surprising. More interestingly, they guess it was an acetogen! I hope you know acetic acid is what makes vinegar sour. Nowadays, 'acetogens' are bacteria that power themselves by converting carbon dioxide and hydrogen to acetic acid and water:

2 COβ‚‚ + 4 Hβ‚‚ β†’ CH₃COOH + 2 Hβ‚‚O

This produces less energy than fermentation, which converts glucose to acetic acid. But hey: sometimes there ain't no glucose around.

The paper says that the metabolism of LUCA could have provided a niche for other microbes living at the time, and recycled hydrogen they made. It's the blue box in the web of chemical reactions carried out by early organisms in the picture at left.

At right you see how if bacteria called methanogens were also also around, they could put methane (CHβ‚„) into the atmosphere, which gets broken down to Hβ‚‚ by sunlight. When this dissolved in water, acetogens can eat it!

The paper is open access:

β€’ The nature of the last universal common ancestor and its impact on the early Earth system, https://www.nature.com/articles/s41559-024-02461-1

The nature of the last universal common ancestor and its impact on the early Earth system - Nature Ecology & Evolution

Integration of phylogenetics, comparative genomics and palaeobiological approaches suggests that the last universal common ancestor lived about 4.2 billion years ago and was a complex prokaryote-grade anaerobic acetogen that was part of an ecosystem.

Nature
Aug 3, 2024 at 8:43amWeb
Show threadPaul H 🏴󠁧󠁒󠁷󠁬󠁳󠁿πŸ‡ͺπŸ‡ΊAug 3, 2024
@johncarlosbaez Does this explain why we like vinegar on chips?
Show threadJohn Carlos BaezAug 3, 2024
@Henrysbridge - Americans have evolved to require ketchup.
Show threadThePsyOfLifeAug 3, 2024

@johncarlosbaez @Henrysbridge
Americans like ketchup on our French fries. We like our chips to be salted and various flavors, but ketchup flavored chips are disgusting.

You'd think after almost 250 years, the Brits could actually learn the language. Jeesh.

Um... that's sarcasm, y'all.

Show threadThePsyOfLifeAug 3, 2024
@Henrysbridge @johncarlosbaez
Who's we?
Show threadPaul H 🏴󠁧󠁒󠁷󠁬󠁳󠁿πŸ‡ͺπŸ‡ΊAug 3, 2024
@ThePsyOfLife @johncarlosbaez anybody who likes vinegar on chips? πŸ˜‰
Show threadThePsyOfLifeAug 4, 2024

@Henrysbridge @johncarlosbaez

That's a thing? There are people, like a lot, who like vinegar on chips. Doesn't that make them soggy? I like my chips crisp.

Show threadPaul H 🏴󠁧󠁒󠁷󠁬󠁳󠁿πŸ‡ͺπŸ‡ΊAug 4, 2024
@ThePsyOfLife @johncarlosbaez Sometimes, chips which are a bit mushy are great with fish and chips.
I'll chuck in some mushy peas as well if you like...
Show threadThePsyOfLifeAug 4, 2024

@Henrysbridge @johncarlosbaez

I guess I can't continue pretending I don't know the different meanings of chips for much longer, but it's been fun while it lasted. Thanks for playing along.

Show threadMarc OlschokAug 3, 2024
@ThePsyOfLife @Henrysbridge @johncarlosbaez
That preference might be related to baked beans on toast?
Show threadThePsyOfLifeAug 4, 2024

@0lschok @Henrysbridge @johncarlosbaez

Because the sulfurous nature of beans produces vinegary farts?

Show threadMarc OlschokAug 4, 2024

@ThePsyOfLife @Henrysbridge @johncarlosbaez

Adding vinegar to beans (and lentils) for better taste and digestibility is quite widespread. But pouring baked beans on slices of toast seem to be typical for the island people living at Europe's culinary fringe.

Show threadPaul H 🏴󠁧󠁒󠁷󠁬󠁳󠁿πŸ‡ͺπŸ‡ΊAug 4, 2024

@0lschok @ThePsyOfLife @johncarlosbaez

Oh, that's only the half of it...

(to be fair, there's plenty of good stuff too - fish and chips is absolutely fine. Just don't ask what goes into sausages... It's unfortunate that in the 20th C we had a few generations who believed in boiling everything to b*gg*ry and beyond!)

And now a terrible confession - I'm quite partial to beans on toast - with a dash of tabasco!

Show threadThePsyOfLifeAug 4, 2024

@Henrysbridge @0lschok @johncarlosbaez

Tobasco, Louisiana's contribution to international cuisine.

Nothing wrong with beans and toast. Po'folk been eating beans and toast for generations.

Ketchup, States contribution to international fine eating.
Fish and Chips, UK's contribution, right?

Show threadJohn Carlos BaezAug 4, 2024
@ThePsyOfLife @Henrysbridge @0lschok - tabasco plus tobacco equals tobasco.
Show threadThePsyOfLifeAug 5, 2024

@johncarlosbaez @Henrysbridge @0lschok

Hmmm... I never thought of it like that before, but when you point it out, it kinda makes sense. By Jove, I think you're onto something!

Show threadMarc OlschokAug 4, 2024

@ThePsyOfLife @Henrysbridge @johncarlosbaez
Yes, Fish and Chips are great (and the British, Dutch and Belgians know how to keep chips at a reasonable size).
Nothing against beans if one wants good performance:
https://www.atlasobscura.com/articles/what-did-gladiators-eat

But soaking toast with it ... I ate it once (as part of a cultural education trip) but it definitely runs against my upbringing with real bread, which rarely exists west of the Rhine.

Gladiator Diets Were Carb-Heavy, Fattening, and Mostly Vegetarian

To survive the arena, they ate a mash of barley and beans.

Atlas Obscura
Show threadThePsyOfLifeAug 5, 2024

@0lschok @Henrysbridge @johncarlosbaez
Don't get me started about bread and processed foods. I was looking at pictures of the '68 DNC, everyone is slim. No obesity.

It's funny how the big American food corporations are basically killing us slowly to milk us for profit. And, how we've convinced ourselves that we need meat in our diet when it provides so little real nutrition.

Show threadPaul H 🏴󠁧󠁒󠁷󠁬󠁳󠁿πŸ‡ͺπŸ‡ΊAug 5, 2024

@ThePsyOfLife @0lschok @johncarlosbaez

..although I understand fish and chips has a more cosmopolitan origin...
https://en.wikipedia.org/wiki/Fish_and_chips

Fish and chips - Wikipedia

Show threadMarc OlschokAug 4, 2024
@Henrysbridge @ThePsyOfLife @johncarlosbaez
Yes, the ingredients are not the problem,
and with a little modification
- replace white beans with lentils
- remove tomato sauce
- add oil and spices
- replace toast with grey bread
this could be tasty.
Show threadDr Daniel, Photon ShepherdπŸ‡ΈπŸ‡ͺπŸ‡¦πŸ‡ΊAug 3, 2024
@johncarlosbaez All Life Is One really is my favourite fact in all of science.
Show threadRowena BallAug 3, 2024

@johncarlosbaez

Amazing, but not surprising, that the LUCA organism was already so sophisticated 4.2 billion years ago! I published a diagram similar to the authors' Fig. 3b in 2019. (It would be nice to think that it inspired the authors.)

The 'tree of life' is widely used both as metaphor and cartoon for the homology of life. Its branches vanish as they grow, so we can see and study directly only its existing tips and such vanished tips for which we have found fossils; the antecedent structure mostly is deduced.

That all life descended from a common ancestor has been widely accepted as a fundamental dogma of biology since Darwin and Pasteur, but this has been questioned. There would seem to be no good reason why cellular life should have arisen just once on Earth. Surely, a 'shadow biosphere' could coexist with the known biosphere - after all, the three domains of life rub along in more-or-less peaceful, often interdependent, coexistence to this day.

I used the diagram and evidence of the early evolution of catalases, from simple Fe^2+ through heme complexes to enzymes, to show that a shadow biosphere could not exist.

If the tree paradigm applies to evolution of the biosphere from LUCA onward, by continuity it must also apply to pre- LUCA evolution. So I also made one for a pre-LUCA tree of life! That was fun!

Show threadBartosz MilewskiAug 3, 2024
@johncarlosbaez This is really surprising: "cellular life was already involved in an arms race with viruses at the time of LUCA"
Show threadjohnkozakAug 3, 2024
@BartoszMilewski @johncarlosbaez Et in Arcadia ego
Show threadDougMerritt (logπŸ˜… = πŸ’§logπŸ˜„)Aug 3, 2024

@johnkozak @BartoszMilewski @johncarlosbaez
Aha, someone making a strong but obscurely-phrased point; surely that's a first. πŸ™‚

"The famous oil painting Et In Arcadia Ego is difficult to find out the inter meaning. It is known as the most difficult workings to interpretation in art history."

As with nature of life 4.2 billion years ago.

Which I think is older than the painting; I'll have to check.

Show threadJohn Carlos BaezAug 3, 2024

@BartoszMilewski - thanks, I hadn't spotted that!

But was there spam?

Show threadMartijn Faassen has movedAug 3, 2024

@johncarlosbaez

@BartoszMilewski

Viruses are like scammers who scam cells to spam themselves so yes

Show threadBartosz MilewskiAug 3, 2024
@johncarlosbaez
What we know for sure is that phishing hasn't started until about 530 mln year ago, during the Cambrian explosion.
Show threadsoaprootAug 3, 2024
@BartoszMilewski @johncarlosbaez Not sure exactly what the evidence is for all these things, but the common belief is that RNA predated DNA. Many viruses have RNA polymerases and the like. So the tendency is to think viruses go back to the shift from RNA to DNA. There probably are some old episodes of the This Week in Virology or This Week in Evolution podcasts which go into it, but I don't remember whether it was a dedicated episode or just mentioned in passing.
Show threadSimon FrankauAug 3, 2024

@johncarlosbaez Wow, interesting!

I'd assumed LUCA would be something more basic. I'd not thought of it as part of an ecosystem with other organisms. Presumably all those others have died out since?

And 2.5Mb?! I guess all the simpler bacteria we have nowadays have derived by shedding a bunch of genes from this common ancestor?

It's kind of mind-blowing.

(Sorry if this is addressed in the paper. I don't have the energy to read it now, so I'm running off your summary. No pressure! ;)

Show threadMarty FoutsAug 3, 2024
@johncarlosbaez I know that LUCA is the prevailing theory but it is worth noting that there is a viable multiple ancestry origin theory that is consistent with evolution. All it requires is that conditions for the origin process to be widespread with a high probability of producing the same result.
Show threadJohn Carlos BaezAug 3, 2024
@MartyFouts - are you talking about the origin of life? LUCA came quite a while after that, so it's almost a separate question.
Show threadMarty FoutsAug 3, 2024

@johncarlosbaez Yes. But if life originated in multiple places then LUCA isn’t necessary because there could be multiple ancestors. Even DNA could have evolved independently in multiple locations, provided that there was similar evolutionary pressure and a high probability of DNA survival.

It’s an unlikely hypothesis but until we know more about how life arose we can’t tell if it was statistically likely and the early fossil record will never be complete enough to rule it out.

Show threadDougMerritt (logπŸ˜… = πŸ’§logπŸ˜„)Aug 3, 2024

@MartyFouts @johncarlosbaez
Mitochondria descended from independent lifeforms that presumably were originally independently-reproducing symbiotes (and possibly parasitic before that).

The point being that, who knows, mitochondria might be descended from something that originated separately from LUCA.

Show threadBarry GoldmanAug 4, 2024

@johncarlosbaez i still don't understand the assumption of a single ancestor. my sense of prokaryotes is that we descend from several populations with different specialties all eveolving in an anastomising net of symbisis.

eventually things shake out to bacteria and archaea

Show threadFrank AylwardAug 4, 2024
@barrygoldman1 @johncarlosbaez I was just at a meeting where this idea was discussed at length. The phrase that kept coming up is "LUCA is a community", meaning that phylogenetic methods cannot prove that the genes existed in the same cell at the same time. So I think that you are essentially correct, but the methods are still valid for tracing broad evolutionary trends
Show threadBarry GoldmanAug 5, 2024

@foaylward @johncarlosbaez if by community we might mean half a dozen different kinds of creatures.

i'll have to review the methods again to see what they say about my idea.

Show threadBarry GoldmanAug 5, 2024
@foaylward @johncarlosbaez now... where did viral protein coats come from?