Meet Luca, the Ancestor of All Living Things

July 26, 2016 11:19 AM

Genes that do the same thing in a human and a mouse are generally related by common descent from an ancestral gene in the first mammal. So by comparing their sequence of DNA letters, genes can be arranged in evolutionary family trees, a property that enabled Dr. Martin and his colleagues to assign the six million genes to a much smaller number of gene families. Of these, only 355 met their criteria for having probably originated in Luca, the joint ancestor of bacteria and archaea.

Meet Luca, the Ancestor of All Living Things

Genes are adapted to an organism’s environment. So Dr. Martin hoped that by pinpointing the genes likely to have been present in Luca, he would also get a glimpse of where and how Luca lived. “I was flabbergasted at the result, I couldn’t believe it,” he said.

The 355 genes pointed quite precisely to an organism that lived in the conditions found in deep sea vents, the gassy, metal-laden, intensely hot plumes caused by seawater interacting with magma erupting through the ocean floor.

See also Study tracing ancestor microorganisms suggests life started in a hydrothermal environment

posted by y2karl (36 comments total)

My name is Luca
I lived on the ocean floor
I lived a long time ago
I don't think you've seen me before

But my genes live in all of you
In rats and squid and mudskippers too
But just don't ask me what I was
It's not that clear just what I was
Just don't ask me what I was
posted by EmpressCallipygos at 11:27 AM on July 26, 2016 [92 favorites]

That is a really clever idea.
posted by It's Never Lurgi at 11:29 AM on July 26, 2016

Damn it, EmpressCallipygos, I was going to do that, but I got stuck looking for terms for up and down directions on the phylogenetic tree, so I could do "I live up-tree from you" or something similar.
posted by Joakim Ziegler at 11:30 AM on July 26, 2016 [6 favorites]

So, wait...is Hell exothermic or endothermic? I forgot...
posted by Chuffy at 11:31 AM on July 26, 2016 [1 favorite]

Came for the Suzanne Vega joke, was not disappointed.
posted by hippybear at 11:58 AM on July 26, 2016 [16 favorites]

...Mom?
posted by Faint of Butt at 12:00 PM on July 26, 2016 [4 favorites]

I think we got the best possible Suzanne Vega joke out of this.
posted by prize bull octorok at 12:15 PM on July 26, 2016 [5 favorites]

Someone needs to find Luca's ancestor right away so we can have the "Luca, I am your father" thing happen.
posted by resurrexit at 12:20 PM on July 26, 2016 [11 favorites]

The Last Universal Common Ancestor has no father. After all, at 4.3 billion years old, that's a long time before there were any sexes.
posted by y2karl at 12:22 PM on July 26, 2016 [1 favorite]

It might have ancestors. The LUCA is the organism from which all current life descends - it isn't necessarily the first organism ever, and almost certainly is not.
posted by Mitrovarr at 12:24 PM on July 26, 2016 [5 favorites]

It could have had a mom, sure...
posted by y2karl at 12:29 PM on July 26, 2016 [1 favorite]

Or, more properly, a clone ?
posted by y2karl at 12:32 PM on July 26, 2016

Hmm. So it looks like we definitely passed through a period where the only life was confined to deep ocean vents, the only question is whether those were the origin or they were the sole survivors of an earlier ecosystem that may have originated in shallower waters and muds. Great post y2karl, thanks.
posted by tavella at 12:32 PM on July 26, 2016 [4 favorites]

But a mom and dad ? Do bacteria and viruses have moms and dads ? I think not.
posted by y2karl at 12:33 PM on July 26, 2016

Last time LUCA was under discussion in a thread here that I participated in (which at the time didn't seem to involve anyone with first-hand knowledge of the field, unfortunately) my reading around on the subject seemed to indicate that there are at least a few prominent scientists who think that the frequency with which horizontal gene transfer has been shown to occur means that there wouldn't be any universal common ancestor—that what we think of as lines of heredity in microorganisms may just fade into the fog of a planet-wide inbred orgy of gene-exchange that occurred outside of reproduction as you proceed back in time.

Does anyone more familiar with the subject than me know if this is true, or if research in the past few years has eliminated that possibility?
posted by XMLicious at 12:36 PM on July 26, 2016 [8 favorites]

...the only question is whether those were the origin or they were the sole survivors of an earlier ecosystem that may have originated in shallower waters and muds.

Well, there was this whole Great Bombardment going on plus this would be way back before there was any land, if I am not mistaken, but rather only oceans.

Unless, of course, these were ponds on extra-solar planets and it hitchhiked on a meteorite.
posted by y2karl at 12:39 PM on July 26, 2016 [2 favorites]

There are some really critical genes that are very hard to transfer horizontally (rDNA, for one). So, even if some genes survive from dead lineages, there might be evidence of a LUCA.
posted by Mitrovarr at 12:40 PM on July 26, 2016 [2 favorites]

My name is Luca
I lived on the ocean floor

Oh so Luca sleeps with the fishes?
posted by prize bull octorok at 12:41 PM on July 26, 2016 [15 favorites]

They were a billion or three point something billion years later....

So, no.
posted by y2karl at 12:52 PM on July 26, 2016 [1 favorite]

Unless, of course, these were ponds on extra-solar planets and it hitchhiked on a meteorite.

From the Vega star system of course.
posted by under_petticoat_rule at 12:56 PM on July 26, 2016 [3 favorites]

the only question is whether those were the origin or they were the sole survivors of an earlier ecosystem that may have originated in shallower waters and muds was wiped out by cleansing nuclear fire after the election of TUCHUS (Trump's Unbelievably Crude, Hateful, Unctuous anceStor).
posted by Johnny Wallflower at 1:00 PM on July 26, 2016

y2karl I believe there are theorized to be 100-300 million years between the condensing of the oceans and the LHB, and as far as I know there was not a point where the surface was so even that it was entirely covered with water. Not a geologist, though. So at least a potential window for shallow-water development before the bombardment. Also -- shallow water wouldn't preclude hydrothermal, would it? We have plenty of hydrothermal springs at the surface.
posted by tavella at 1:01 PM on July 26, 2016

Well, you are better informed than am I, so I just don't know...
posted by y2karl at 1:04 PM on July 26, 2016

Oh cool!

*clicks through*

"By Nicholas Wade"

Oh. Oh well. I wonder what he's screwed up.
posted by biogeo at 1:06 PM on July 26, 2016

From the Vega star system of course.

Sadly, no, LUCA is far older than Vega.
posted by y2karl at 1:15 PM on July 26, 2016 [2 favorites]

Maybe now that they've found Filthy LUCA, Dirty EZIO won't be far behind...
posted by Greg_Ace at 1:38 PM on July 26, 2016

After reading: I love this topic, though I'm nothing like an expert in it, and I wish Wade had done a better job explaining it. Two of the scientists quoted alluded to the important distinction between original/early life and LUCA, but that distinction didn't come across as clear to me in the article. Basically, if you imagine a big Italian-American family reunion, maybe everyone is related by descent from one pair of great-grandparents who immigrated; those great-grandparents would be the last common ancestors for the family. But they also have a long chain of common ancestors back in Italy. So at least part of this research seems to be about trying to figure out just how long that chain of ancestry is. From the article:

Luca and the origin of life are “events separated by a vast distance of evolutionary innovation,” said Jack Szostak of Massachusetts General Hospital, who has studied how the first cell membranes might have evolved.

So the suggestion by William Martin is that this "vast distance of evolutionary innovation" was compressed in a relatively short amount of time, geologically speaking. Others like John Sutherland think it had to have taken longer. This isn't a new debate, and has been going on for at least fifteen years since I started paying attention. My impression is that over time the weight of the evidence seems to be supporting the idea that early evolution proceeded extremely quickly, but I'm not well equipped to evaluate it.

The question of horizontal gene transfer and other quirks of microbial evolution make things much murkier. We like to think of a tree of life, but for microbes the branches often converge. For the math/CS types, it's probably more appropriate to think of a directed acyclic graph; for the anatomy types, think of the tree as full of anastomoses; for Darwin fans, maybe he was closer with his "tangled bank" line than with the tree metaphor. Tracking individual genes rather than species/strains helps untangle things to some extent, but from what the molecular biologists I know tell me, there's plenty of instances of novel genes (sensu protein-coding sequences) evolving by the duplication and combination of functional motifs elsewhere in the genome (at least in eukaryotes), so even for single genes, the graph of ancestry is not necessarily a perfect tree.

In human evolution, people sometimes like to talk about last common ancestors like "mitochondrial Eve" and "Y-chromosome Adam," but because of the fact that the graph of human ancestry also has reconvergence ("inbreeding" even if at several degrees of distance), the fact is there was no one single common ancestor, but a small population of individuals, any one of whom has equal claim to the title "last common ancestor." To me, at least, it seems likely that this is probably the case with LUCA as well: that there was a rather heterogeneous set of organisms which, thanks to things like horizontal gene transfer, any one of which has an equal claim to being LUCA. But this is an amateur, not professional, opinion.

More fun concepts in early evolution: Urmetazoan, common ancestor of all animals, and Urbilaterian, the common ancestor of all bilaterally-organized animals.
posted by biogeo at 2:31 PM on July 26, 2016 [7 favorites]

Here it is: The practice of classification and the theory of evolution, and what the demise of Charles Darwin's tree of life hypothesis means for both of them (2009) by W. Ford Doolittle:

In fact, LUCA is illusory. If there is as much LGT as we WOLers think there is, the proper way to model prokaryotic evolution over 4 Gyr is as a single, albeit highly structured, recombining population, not an asexual clade. To accept this is to abandon the concept of a single tree with a single root (or at least a single rooted tree of genomes) because it means that different gene families trace to gene-family-specific ancestors that existed in different genomes at different times in the past. There will have been no single common ancestral cell whose genome harboured a direct ancestor (either the last common ancestor or their lineal predecessors) of all the genes present in all genomes today. Indeed such an ancestral cell need not have contained lineal ancestors of any of the genes around today, and is thus basically unknowable. The many attempts one still sees to reconstruct its genome are groundless, and to say the LUCA was a population is meaningless. Of course populations such as ‘all prokaryotes today’ have populations (all prokaryotes Y years ago) as their ancestors in this loose sense, but there is no principled way to designate the population at some particular value of Y as ‘LUCA’.

Planetary super-orgy, I'm tellin' ya.
posted by XMLicious at 2:52 PM on July 26, 2016 [7 favorites]

Well, not to contradict anyone, for I am far too ignorant, there is this from the second link:

The result is important because it identifies specific groups of bacteria (clostridia) and archaea (methanogens) that carry early versions of these genes, meaning they are very ancient and may be similar to the very earliest organisms that gave rise to the separate bacterial and archaeal lineages.

More importantly, the nature of the genes that are conserved tells an amazing story about the kind of environment in which this last common ancestor lived – including how it extracted energy to survive and thrive. The study suggests that the world inhabited by these organisms nearly four billion years ago was very different to the one we live in now. There was no available oxygen, but according to the genes, this common ancestor probably obtained energy from hydrogen gas, presumably made by geochemical activity in the Earth's crust. "Inert" gases including carbon dioxide and nitrogen would have provided the key building blocks for making all cellular structures. Iron was freely available, with no oxygen to turn it into insoluble rust, and so this element was used by many enzymes in the early cell. Some of the genes are believed to be involved in adaptation to high temperatures, which suggests these organisms evolved in a hydrothermal environment – perhaps equivalent to modern hydrothermal vents or hot springs, where some bacteria still thrive.

But, on the other hand, I have learned more today. Among other things, Vega is a very interesting star.
posted by y2karl at 3:00 PM on July 26, 2016

I can also see how this could help us better understand and search for lifeforms on other planets.
posted by Greg_Ace at 3:50 PM on July 26, 2016

Among other things, Vega is a very interesting star.

I know, right? And so underrated.
posted by flabdablet at 7:45 PM on July 26, 2016

I just finished Life Ascending a few weeks ago, the first few chapters of which are origin of life biochemical speculation, and am super excited that what I learned from a five year book isn't obsolete! Yet.

They discuss a lot of what I hadn't heard before and isn't 100% clear now: the difference between hot acidic vents (more famous and discovered first) and alkali vents. Martin, who authored this study, was a big believer in alkali vents and this is what the genetic analysis apparently supports.

The argument is that these contain cell-sized porous rock formations *and* the raw materials and conditions for the basic chemistry, along with mineral catalysts. This is the proposed solution to the idea that the ocean would dilute out and starting materials--that near the vents they'd actually be quite concentrated. Obviously the skeptic in the NYT piece, Sutherland, knows this argument and doesn't buy it but I wish they'd gone into it in the piece, along with more about the chemistry and why Sutherland doesn't buy the pathways proposed that aren't really discussed here. (Essentially I'm asking for a book length treatment in the Tuesday Science Times, well written for my level of knowledge and treating both sides fairly.)

I'm also curious about this:

Luca and the origin of life are “events separated by a vast distance of evolutionary innovation,” said Jack Szostak of Massachusetts General Hospital, who has studied how the first cell membranes might have evolved.

From Dr. Martin’s data, it is clear that Luca could manage the complicated task of synthesizing proteins. So it seems unlikely that it could not also synthesize simpler components, even though the genes for doing so have not yet been detected, said Steven A. Benner of the Foundation for Applied Molecular Evolution. “It’s like saying you can build a 747 but can’t refine iron.”

To my chemist (but not biochemist let alone biologist) background, synthesizing proteins seems easier than "simpler" components. Amino acids can form spontaneously under certain conditions, and there are a relatively small number of reactions that are needed to build chains this. Synthesizing simpler components in modern life generally requires proteins, and often complex ones, to do so. Proteins are big and other thing may be small, but you just need to know one trick to build proteins. It's like the difference in skill levels required between building something out of interchangeable blocks like legos, and chiseling it out of a block of marble.

To me the plausible origin of life argument would be someplace where the non-protein components are available abiotically, giving a scaffold for life to build upon. Later, when there's enough protein and RNA and eventually DNA to really get going, organisms evolve ways to synthesize themselves instead of picking them up off of "weird" places like the ocean vents.
posted by mark k at 10:42 PM on July 26, 2016 [4 favorites]

The Late Heavy Bombardment will be the name of my stoner sludge band.
posted by gamera at 11:46 PM on July 26, 2016 [4 favorites]

Among other things, Vega is a very interesting star.

I know, right? And so underrated.

Fixed that for ya!
posted by y2karl at 10:45 AM on July 27, 2016

PS. Vega: The Once and Future North Star
posted by y2karl at 10:57 AM on July 27, 2016

The Ars Technica article covering this research published in Nature Microbiology, authored by John Timmer; John became Ars Technica's science editor in 2007 after spending 15 years doing biology research at places like Berkeley and Cornell. discusses the methodology more specifically than the articles in the OP, and particularly the complexities introduced by horizontal gene transfer. Though, he doesn't seem to question the view of LUCA as a particular organism or species. However he does seem to agree with the skeptic in the NYT article by concluding with,

It's important to emphasize that this data doesn't mean life was started at a geothermal event; the origin of life was well before LUCA. But it does suggest that geothermal vents provided life an environment in which it could thrive long enough to start evolving some of the genetic toolkit that it still relies on today.

posted by XMLicious at 1:30 PM on July 27, 2016 [2 favorites]