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For James, our master of microscopes, the immense breadth has made ciliates a bit of an obsession. Whether he’s hunting down a rare species, or documenting the behavior of something more familiar, there’s always something spectacular in this group.

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Go to to get a   free trial and 10% off your first  purchase of a website or domain. Here’s a little microcosmos joke for you.

What has two types of nuclei  and is covered in hair? This guy. Well, never said it was a good joke.

But that hair and those nuclei have been beguiling  scientists for centuries, so today, we are going   to explore how two features that are so common  to so many organisms can remain so mysterious. The organism we opened this video  with is called Stentor coeruleus,   and it belongs to a broader class of single-celled  eukaryotes who are part of the phylum Ciliophora. But we know them as ciliates.

This group of organisms is  vast and incredibly diverse. There are giants, like stentors, that can  sometimes even be seen with the naked eye. There are armed ciliates, like this suctorian with   tentacled arms protruding from  their bodies to capture food.

And other ciliates, like  these paramecium bursaria,   fill up their body with endosymbiotic algae  that exchange nutrients for protection. For James, our master of microscopes, the immense  breadth has made ciliates a bit of an obsession. Whether he’s hunting down a  rare species, or documenting the   behavior of something more familiar, there’s  always something spectacular in this group.

Everything ultimately revolves around ciliates. And that puts him in good company. One of the original masters of microscopes  was Antonie van Leeuwenhoek, a Dutch tradesman   who used his simple microscopes to examine  everything from rainwater to his own waste.

Leeuwenhoek’s writings contained some of  the earliest descriptions of ciliates,   like this bell-shaped Vorticella. In 1675, Leeuwenhoek noted something interesting  in one of his samples, which he called: “incredibly thin little feet.” Of course, the thin little feet he was  writing of, were not actual feet. They were hairs, or more specifically, cilia.

Cilia are, of course, one of the main  defining features of ciliates,   though they are not unique  to this group of organisms. In our own bodies, cilia are found on a  number of cells, like sensory hair cells. Leeuwenhoek’s observation marks what is perhaps  one of the first descriptions of a cell organelle.

They are made from tiny tube structures called  microtubules, which are arranged to form a central   core that is then surrounded by  a ring of more microtubules. The whole thing is encased in a membrane  that is attached to the cell’s membrane. And in ciliates, the hairy structure that forms can be quite distinctive and, of course, practical.

You can see them whirring here  along the side of this amphileptus. The coordinated movements of the cilia can steer the organism through the microcosmos. In Euplotes and other ciliates, cilia can  bundle together to form structures called cirri,   which they can also put to  work as they swim around.

And cirri and cilia alike can  also help ciliates with eating. From one side, this condylostoma looks  like an eel on the hunt for food,   with cilia whirling around its oral  apparatus to help it gather food. In some ciliates, those hairs  act like a trap of sorts,   helping to both bring in food and  filter it through to the organism.

So you might wonder…how did ciliates  get to be cilia-y in the first place? Who was the first microbial genius  that invented these hairy structures? Well, we do not know.

Bacteria do have their own hair-like structures,   but they are distinct from the  cilia found on eukaryotes. They evolved separately. But somewhere in the past was an organism  known as the Last Eukaryotic Common Ancestor.

This is the eukaryote at the root  of all the eukaryotes we know today, including ourselves. We do not know the identity of this  organism, but as our ability to study   modern day organisms has expanded with new  tools to understand them at the genetic level,   there’s been a mishmash of features  that we can trace back to this ancestor. And one of those features is, yes, cilia.

The Last Eukaryotic Common  Ancestor likely had them. Which means that their origin traces back  to something even older and more mysterious,   something we still do not have the means to identify. What makes this even more interesting is that  today, if we look across all the descendants   of this mysterious ancestor, we can find plenty  of organisms that do not have cilia, like amoeba.

Which means that as useful as cilia are, they have  also been disposable to certain lineages. And that is fascinating in its own way  because it reminds us that evolution   is messy, and it doesn’t necessarily  proceed in a straightforward path. A certain feature can spawn a number  of advantages for an organism,   that in turn forms an incredible array  of species that contain that feature.

And then, by some mysterious evolutionary means,  that feature can become unnecessary for some   species, forming its own divergent  corner of diversity through loss. But when it comes to messy evolution,  ciliates have even more to offer. Like the fact that for some strange  reason, many ciliates have two nuclei.

One is called the macronucleus, and  the other is called the micronucleus. As you might have gathered from the names, the  macronucleus is big, the micronucleu, small. But their differences, it turns out, go a lot deeper than that.

Some of the early descriptions  of these two different types of   nuclei actually came from descriptions  of ciliates going through conjugation,   which is the ciliate approach to sexual reproduction. And over time, scientists have found more and more difference between   the macronucleus and the micronucleus  going far beyond their size. The macronucleus contains the genes  that get expressed in the organism,   encoding the proteins that  allow it to survive.

But something weird happens when  ciliates with a macronucleus reproduce: their macronucleus gets destroyed in the process,   disintegrating before it can  pass down its information. Which leaves us with a question: how do you get the new offspring? Well, that is the job of the micronucleus.

It holds the genes that are passed down to  the offspring, along with extraneous bits of   DNA that either don’t code for anything  or aren’t expressed in the organism. As the new offspring forms, it constructs  its new macronucleus from the micronucleus,   using bits of the old macronucleus to  figure out what those extraneous bits of   DNA in the micronucleus are so they can get  cleared out by enzymes called transposases. It’s all kind of complicated and kind of redundant, right?

Like, why go through this process of destroying  one nucleus and recreating it from another   nucleus that also has a whole bunch of  unnecessary bits that need to be cut out? Well, of course, it’s hard to know. Most of the information we have about this  process comes from three ciliate species:   paramecium, tetrahymena, and oxytricha.

Researchers have also been  expanding to look at blepharisma,   which is more distantly related to those three. That gives them a little bit more insight  into what the ancestral ciliates might have   looked like, but still leaves us far from being  able to understand the point of this system. In 2023, two researchers presented  their own hypothesis for how this   system may have evolved in a paper titled “How ciliates got their nuclei.” In their speculation, there was once a small  ancestor with just one nucleus and a transposase.

Over time, perhaps that small,  single-nucleus ancestor became larger. And as it became larger, it demanded more  and more protein production to survive,   leading to the creation of more than one nucleus. And then, perhaps, one of  those nuclei became larger   and capable of holding multiple copies of its DNA.

It’s now a nucleus that has all the means  to provide the proteins the organism needs,   and so the other smaller nucleus can go quiet. There are still transposase  enzymes in these nuclei,   but they’ll only be active in the larger nucleus. So the bits of DNA that those enzymes normally cut  out will accumulate in the smaller, quiet nucleus.

And so the genetic sequence in  that smaller nucleus also begins   to look less and less like the  ancestral DNA of the organism. But the trouble is that the larger nucleus  is too large to divide during reproduction,   so it keeps getting lost. Well, luckily there’s that other smaller  nucleus, with all the components you   need to reconstruct the larger one.

It might  take a little bit more effort, but it works. Again though, this is just a hypothesis,   it is one potential story that boils down  a mysterious history into a series of   steps that makes some sense, but that we do not know enough to know if they are true. To know more, scientists will have to continue  studying ciliates and gathering more of their DNA.

And every observation fills in a little more  of the puzzle of how ciliates came to be,   which in turn tells us just a little  bit more about how we came to be. And we’ll talk more about  that in our next episode. But for now, we just want to leave you with  our friends, the ciliates, who so generously   tell us about themselves just by existing and  swimming across our view under the microscope.

Thank you for coming on this journey with us as  we explore the unseen world that surrounds us. And thank you to Squarespace  for sponsoring this episode. If you don’t know what Squarespace is,   it’s a powerful all-in-one platform  for creating your own website.

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