The Great Eukaryotic Melee

Cat fight! Mrowwwr! Hisssssss!

Every now and then, you can capture a snapshot of the scientific process at its worst (and paradoxically, its best, too). The trick is to look at the Letters or Perspectives section of your favorite scientific journal.

In this case, I happened to come across an argument between two sides in what I will call the Great Eukaryotic Melee (there are probably more than just two sides in this debate, but only two are reflected on these pages). Actually, the debaters seem to be rather more well-behaved than I suggested above, but it is true that these fights do sometimes turn ugly.

The central issue? How did Eukaryotes evolve. Let’s review some basics.

We are Eukaryotes. This means that our cells have a nucleus, contain several organelles made of membrane material (which act like internal compartments), and especially, use mitochondria as their powerhouse. All animals are Eukaryotes, as are all plants and fungi. There are also some single-cellular eukaryotes that don’t quite fit the definition of plant, animal or fungus, which we’ll just lump together as “protists”, to annoy the people who study them. Eukaryotes are good at manipulating their outer membranes to take on different shapes and engulf small cells or particles.

To define a group, we also need to consider what is not in the group. The non-eukaryotes are collectively called prokaryotes. Prokaryotes include the bacteria, but also a lot of other comparatively simple single-celled critters that would be offended to hear us talk about them all as if they were the same as bacteria.

…If they could hear.

…Or get offended.

The uniting factor in all prokaryotes is their lack of a nucleus (their DNA just sits inside the cell, unprotected), internal compartments and mitochondria.

BTW, if a group of organisms is defined only by what it lacks, and not by some positive list of properties, you should expect the definition to fail soon.

Strangely, the big question at stake here is not about the nucleus, even though any elementary bio text will define eukaryotes by the presence of a nucleus. No, the big debate is about the mitochondria, the organelle that uses oxygen to make the energy-dense molecule ATP.

You see, the mitochondria seem to be prokaryotes.

Let’s read that sentence again, together: the mitochondria seem to be prokaryotes. Living bacteria-like cells, inside each of our cells. Oh, and chloroplasts, the light-harvesting organelles in plants, seem to be bacterial too – although I want to focus on the mitochondria for now.

Since about 1910, there have been many scientists who advocated this position. Lynn Margulis made the best defense of the theory in 1967. Lynn noticed that the mitochondrion has unique features. It has a double membrane, several bacterial proteins, and most telling, a ring of its own DNA.

Prokaryotes also have DNA in a ring-shape, whereas Eukaryotes keep their DNA in the form of rod-like chromosomes. Furthermore (cutting ahead several years in the analysis), the DNA of mitochondria has a distinctly bacterial character. In fact, we can localize it. Recent work has shown that mitochondria are most similar to a group of bacteria called Rickettsiales.

So, some distant ancestor of our cells somehow engulfed a distant ancestor (or a cousin of the distant ancestor) of a Rickettsian bacterium, failed to digest it, and began using it to harvest energy.

The current debate is: how? It’s a huge question, because the endosymbiotic hypothesis (as the mitochondrion origin theory is known) carries with it several mysteries. First of all: what kind of cell originally engulfed the ancestor of the first mitochondrion? Already we have a problem, because all modern eukaryotes have more than one important difference from the prokaryotes. They aren’t just cells that contain mitochondria; they are cells with mitochondria that also have nuclei and organelles and other interesting features. Where did all those other differences come from?

The two basic answers are: before or after. Either the eukaryotic ancestor already had those other qualities when it ate the first mitochondrion, or it gained them afterward, possibly in response to its new acquisition. Or, of course, it could be a mix of the two: some characters were gained before, and some after.

Fortunately, each of these possibilities carries predictions with it, so they should be easy to test, right?

If the other features of Eukarya evolved before the endosymbiosis, then we should be able to find some single-celled critter that has a nucleus and organelles etc., but no mitochondria. Plus, its DNA should be similar to ours, but not nested withing the Eukaryotic evolutionary tree.

If the other features evolved afterward, then we should see the opposite: We should see various species of mitochondrion-bearing cells that don’t have a nucleus or other organelles. Again, the genetic evidence should tell us that these hypothetical creatures sit just outside of the evolutionary tree of the Eukaryotes.

So what do we find?

Ha ha ha! We don’t know. We can barely agree on which prokaryotic group our eukaryotic cells are closest to. Some say they are like true bacteria, while others say they are most like another group called the archaea, although the genetic information favors the latter.

There is one potential “missing link”. The bacterial group called “Plantomycetes” have structures that look like a nucleus and membrane-bound organelles, but no mitochondria. That would support our “before” hypothesis: Eukaryotes already had a nucleus etc. when they engulfed the first mitochondrion. Except, the genetic information suggests that Plantomycetes aren’t very closely related to Eukaryotes. Also, their putative nucleus and other organelles have been called into question. They might have evolved separately.

So where do we stand today?

Well, there is a recently discovered species called “Lokiarchaeota” which might fit the bill. The problem is, we have no known examples of it. It was found by genomic analysis of a sample of dirt from a geological core. That is, they analyzed the dirt for DNA fragments and reconstructed what they found. No living Lokiarchaeotans were ever observed. So we don’t know much about the critter. And this is where the current argument (remember our snapshot of science?) begins.

In the latest issue of Science (27 May, 2016), Sven B. Gould wrote a complaint about a Perspective written a couple of months ago by a group of scientists (Steven G. Ball, Debashish Bhattacharya, and Andreas P. M. Weber, 12 Feb 2016). We’ll call this latter group BBW for short, although I’m sure somebody will get offended. No pun is intended.

Anyway, BBW had noted in a letter to Science that the Rickettsians are generally endoparasites themselves. They get inside of the cells of various animals or protists and can live there for a while, taking advantage of their hosts’ “hospitality”. There doesn’t seem to be evidence that the host gains much benefit from the Rickettsians.

They also point out that the Lokiarchaeotans have many genes associated with “membrane remodeling, vesicular trafficking, and endocytosis”. That suggests that they can make organelles and do some other Eukaryote-ish things, like engulfing foreign cells. Sounds promising, right? Specifically, this would seem to support our “before” hypothesis again. A cell that could engulf other cells fell prey to an endoparasite. BBW suggests that an “arms race” ensued, in which the host tried to digest the parasite and the parasite tried to survive, until they finally learned to get along and share resources.

Gould objects on several counts. First of all, he says that Lokiarchaeotans don’t actually have genes for endocytosis. Since that is a direct contradiction of what BBW claims, and I assume they were basing it on actual evidence, I’m not even going to begin to adjudicate between them. Secondly, he points out that in modern Eukaryotes, the kind of endocytosis we need for the BBW hypothesis to be correct is actually dependent on the presence of mitochondria. Thus, the mitochondria-less ancestor of Eukaryotes couldn’t have engulfed anything, or at least not in the way that BBW suggested. Finally, he argues that the BBW hypothesis does not explain why there are no Eukaryotes that lack mitochondria.

Presumably, Gould supports a model of Eukaryotic evolution in which a far simpler organism somehow engulfs the first mitochondria because the mitochondial metabolism was mutually beneficial, not because it was invaded by a paratsite.

It gets weirder. BBW replied to Gould in the same issue, saying that yet other studies suggest that “Mitochondrial Ancestor Was an Energy Parasite” (Wang and Wu, 2014, Gabaldon and Huynen 2003) and only later became useful to the host. The necessary metabolic genes for that innovation were transferred to the mitochondrion by the host, they claim.

I can barely capture the entire argument in this short format. But I need to explain one last thing before I move on: the spat isn’t just about mitochondria, because mitochondria aren’t the only organelles that have evolved from a bacterial ancestor. Chloroplasts – the photosynthesizing structures in a plant’s cells – seem to have evolved from yet another, wholly different bacterial ancestor (which shockingly, might be related to Chlamydia), and that’s a whole other can of worms that this short exchange busts open.

Still, we can learn an important lesson from this argument, because we are seeing the raw version of the story, straight out of the scientific literature. When the newspapers print a story about some scientific achievement, they’re only giving us a small part of the story. They make it look certain and settled. Similarly, text books make the science look easy. This is because both are prone to ignoring the underlying debates that go into scientific advances. The difference is that in a well-written text book (and I admit there are poorly written texts), the information we are given is the product of decades of debate, in which all the details are sifted, compared and fought over by the scientific community. The layman might choose to argue with these conclusions, but it is likely that all the relevant arguments have been seen and countered before. What we see is settled, not by fiat, by careful analysis. When we are told, for example, that vaccines are safe and effective, it is because they’ve already hashed out the details.

By contrast, many newspapers are looking for a snapshot of news-worthy triumph. The reader is likely to miss the chaotic reality that makes science ultimately dependable – and so much fun.


  • Ball, Steven G., Debashish Bhattacharya, and Andreas P. M. Weber, 2016a. Science, 351(6274):659-660.
  • Ball, Steven G., Debashish Bhattacharya, and Andreas P. M. Weber, 2016b. Science, 352(6289):1065-1066
  • Gabaldon, Toni and Martijn A. Huynen 2003. Science 301(5633):609
  • Gould, Sven B. 2016. Science 352(6289):1065
  • Wang, Zhang and Martin Wu, 2014. PLoS One, 9(10)

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