What Was the Ancestor of Everything? (feat. PBS Space Time and It’s Okay To Be Smart)

Part of what draws us to the study of natural history is our desire -- our drive -- to understand our origins. The more fossils that we can find and study, the more branches and twigs we can add to the tree of life -- that web of relationships that connects all organisms, living and extinct. But fossils can only get us so far.

As any astrophysicist will tell you, the story goes back way farther than any fossil. The story of life actually begins with, well, the beginning of everything. In the aftermath of the Big Bang the universe was an energetic, structureless mess.

But that mess pulled itself together into atoms and stars and galaxies and planets and, finally, into life. How did these little eddies of order form in a universe otherwise prone to increasing disorder and chaos? I’m Matt O’Dowd from PBS Space Time, and you can learn all about the physics of the origin of life in a video over on our channel Just follow the links.

But for us here on Eons, the search for our origins go back to a single common ancestor -- one that remains shrouded in mystery. If you trace all of the branches on the tree of life backward, you realize they all come from the same trunk. That initial point, before anything branches, is a single species.

The first species. Darwin himself theorized that such a thing once lived. He called it a “primordial form into which life was first breathed.

” Today, scientists call it the last universal common ancestor, or LUCA. LUCA isn’t the first thing to have lived. Instead, it’s the common ancestor of everything that’s alive today.

It’s the ancestor of everything we know. Today, Eons is teaming up with our friends at Space Time and It’s Okay to Be Smart to explore the origins of life. And our journey begins with LUCA.

Even though Darwin suggested that there was a universal common ancestor, we couldn’t even guess what it might have been -- until we started to master genomics, the science of mapping and studying the genetics of all living things. Today we know that all life uses the same molecules of RNA, DNA, and protein. And the genetic code that’s responsible for making that stuff is basically universal, from bacteria to humans.

That’s one of the best arguments to support the notion that everything came from the same place. It’s also why most of the research that’s gone into learning what LUCA was has involved comparing the genomes of all kinds of living things, to see what else they have in common. One of the first to take this approach was American biologist Carl Woese In 1977, he discovered the existence of organisms that would make up a whole new domain of life, and a key to the search for LUCA.

He discovered archaea. They’re a group of prokaryotes -- simple, single-celled organisms that are vaguely similar to bacteria. But they turned out to be so diverse, and so different from any other living thing, that Woese proposed a new tree of life -- one that divided life into three domains: archaea, bacteria, and eukaryotes.

And, he said, where those three main branches converged, there was LUCA. But he saw the three domains arising not from a single cell, but from a chaotic environment, more than 4 billion years ago, when cells didn’t quite exist yet. In this scenario, he proposed, there were extremely simple things that were even more basic than cells.

He called them progenotes and envisioned them as tiny scraps of genetic information, surrounded by a membrane. These progenotes wouldn’t have been complex enough to create true offspring. They might have been able to copy their genetic material, but not accurately.

So instead, they may have just floated about at random, constantly swapping little snippets of genetic code among themselves. Sometimes, that genetic info might have worked well for a progenote, and could be copied. Other times, not.

But out of this basically random transfer of information, Woese thought, some of the key elements of life could have arisen. For instance, the genetic code that makes up genes as we know them could have come about pretty early. But that information might have been stored in RNA, not DNA as it is today.

To explain how that might have worked, here’s a biologist I know who specializes in RNA: Dr Joe Hanson, host of It’s Okay to Be Smart: Now, RNA, in addition to storing information, can do stuff – biochemical reactions – like we see in the ribosome, where RNA is used to not only code for, but also build, proteins. Early on, RNA machines like the ribosome would have evolved alongside genetics version 0. 1.

So, it’s likely first life arose and evolved in this so-called RNA world, and only began storing genetic information in DNA later on. For more on how this happened -- and other theories about how life first arose on Earth -- check out our video over on It’s Okay to Be Smart. So, instead of being a specific organism, or even a group of things.

Woese thought that LUCA was the whole process by which progenotes acquired the genes to make these essential molecules. And from them would have come three lineages that evolved into modern bacteria, archaea, and us eukaryotes. Now, Woese’s view of LUCA hasn’t been abandoned, but many scientists have moved away from it.

That’s partly because, when Woese was publishing these ideas, genetic sequencing was just coming of age. Back then, only a handful of genomes had been sequenced. And now we’ve mapped the genes of thousands of living things.

And that means we can try looking for LUCA in new ways -- like, by lining up genomes from across all of the domains of life and comparing them to see what they have in common. If a gene appears in basically every living thing -- so it’s considered universal -- then it must have come from LUCA . .

. or so the thinking goes. So, many researchers who study LUCA are trying to reconstruct its genome.

One way to do that is by finding what they call the minimal genome -- the smallest amount of genes that a cell can have and still survive. Since these most basic, essential genes are thought to have come from LUCA, if we could identify them, that could tell us how LUCA looked and lived. This work has been spearheaded mainly by researchers in Maryland who have studied the genomes of bacteria like Haemophilus and Mycoplasma.

And based on what those organisms had in common, the team proposed back in 2003 that LUCA probably had 5 or 6 hundred genes. Those genes would have provided for a simple metabolism and a genome based on RNA -- but not for making and copying DNA. Now, as genomes go, that is tiny.

A few modern organisms do have about 500 genes, but they are parasites that steal what they need from their hosts instead of using genes to make stuff. Meanwhile, the bacterium E. coli has around 5 thousand genes, and we humans get about 25,000.

Could LUCA survive on its own with so few genes? Well, another study done in 2006 found that LUCA would likely have had more like 1000 genes, maybe around 15 or 1600. According to this slightly more recent take, our common ancestor might have been a little more complex and may have seemed more familiar -- to microbiologists at least.

That means a genome based on DNA, ribosomes to translate the genetic code, and a metabolism that could break down sugar for energy. So, the basics of biochemistry as we know it. And Joe talks a lot more about that, too, on It’s Okay to Be Smart.

Now, a lot of this minimal-genome research took place at the turn of the millennium -- around the same time Woese was thinking about LUCA. But in the past 20 years, the genetic revolution has redrawn the tree of life. Recently, many scientists have begun to argue that the tree of life should have two main branches, with bacteria on one branch, and archaea plus all of the eukaryotes on the other.

That’s because, the more we learn about genomics, the more it seems that all modern eukaryotes are genetically more similar to archaea than to bacteria. In fact, many researchers now believe that archaea are our ancestors. So of course, this has enormous implications for what LUCA was, too.

In this case, LUCA would sit just below where those two main branches separate, before eukaryotes even formed. And based on this new line of thinking, a surprisingly complete picture of LUCA was published in 2016, in the journal Nature Microbiology. Here, evolutionary biologists based in Germany compared the genomes of more than 130 archaea and over 1800 bacteria in an attempt to reconstruct LUCA’s genome.

Keep in mind here, in the two-branch model, archaea and bacteria are the most distantly related forms of life on Earth. So, if you can find any gene in both archaea and bacteria, then there are two possibilities: Either the two groups traded genes at some point, which prokaryotes sometimes do, or they both inherited that gene from LUCA. The researchers looked for genes that appear in two different groups of archaea, and two different groups of bacteria, reasoning that if a gene shows up in all four of those places, it must go back pretty far.

Now, this is different from the minimal genome approach, because it tries to identify the oldest genes, not the ones that everyone has. And the genes that were recovered in this research suggest that LUCA lived in … hydrothermal vents. How do they know?

Well for one thing, they recovered a set of genes that we know are used by extremely ancient groups of archaea and bacteria that live in oxygen-free environments, where they metabolize hydrogen gas and carbon dioxide into methane. Hydrogen gas is hard to find on Earth, but it can come from deep sea vents; so that’s one clue. Other genes they found use metals like iron, nickel, and molybdenum in order to function.

And these are all found in the same kind of environment as hydrothermal vents. Scalding-hot vents full of metals and sulfur might seem pretty hostile. But our earliest ancestor might have called these places home.

Now, how could that be? Like, we don’t metabolize hydrogen and CO2 to methane. And neither do most of the organisms we know.

So how could the ancestor of everything have been so different from us? Well, it’s at least possible, because genes are often lost over time. As creatures evolve and adapt to new environments, lots of old genes aren’t always needed.

That’s basically why cats have genes to make fur, and not scales. So by the same token, long after molecular oxygen became available on Earth, about 2. 5 billion years ago, many of LUCA’s descendants were able to lose the genes for metabolizing hydrogen and CO2, and still live comfortably.

Now, as awesome as this picture of LUCA is, it’s only one possible picture. It’ll be a long time before we know enough to agree on one single model. Both the progenote model and the minimal genome idea have proven useful to guide our thinking, but they probably don’t represent the true LUCA.

And not everyone agrees that LUCA lived in hydrothermal vents either. There’s plenty more research to be done. Because the search for LUCA just might be the one quest that defines the purpose of natural history -- to reveal to us where we came from.

Now, to explore other facets about the origin of life, I encourage you to check out the companion videos to this one, on PBS Space Time and It’s Okay to Be Smart. Links are in the description. And as always, I want to know what you want to learn more about!

So leave me a comment below, and don’t forget to go to youtube. com/eons and subscribe And also, tell people about us. Please.

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