Friday, April 17, 2015

Story-telling and the origin of eukaryotes

Austin Booth and Ford Doolittle have just published a paper that discusses the origin of eukaryotes (Austin and Doolittle, 2015). They point out that many of the stories about this event are not grounded in fact. Read the paper.
Writing for public audiences, and often even for themselves, biologists are not loath to make simplifying claims about uniqueness and importance that are rhetoric disguised as fact. Such generalizations serve purposes in the doing of science, but are often not themselves testable scientific claims and are subject to biases. Evolutionary biology may be especially vulnerable to hype, as suggested by the frequency with which revolutionary evolutionary claims in top-notch journals are debunked. Additionally, anthropocentrism, as it grades into "zoocentrism" and then "eukaryocentrism," surely remains a subtle distorter of objectivity.

Our aim here is to critique general claims about the uniqueness and special importance of eukaryogenesis, with an aim to making them more open to question and conceptual and empirical analysis. We ask (i) whether eukaryogenesis entailed such a "genuinely unlikely sequence of events" as to justify belief in its uniqueness as a process, (ii) if, as is often claimed, eukaryogenesis has a problematic or unique theoretical status in evolutionary biology, (iii) what intrinsic features might have conferred on eukaryotes their presumed "richer evolutionary potential," and (iv) if this greater potential might be just a presumption, an illusion reflecting eukaryocentric bias.
There are many useful ways of understanding evolution, and their articulations can be intellectually valuable and experimentally fruitful. We advocate a more self-conscious pluralism that would require not that we stop telling eukaryogenesis stories but that we do recognize them for what they are. We do not claim to know whether there is any best story, any theory by which the apparent differential success of eukaryotes can be objectively probed and causally rationalized. What we have questioned here is whether premises of existing theories have been objectively formulated and whether, despite widespread acceptance that eukaryogenesis was "special," any such notion has more than rhetorical value.


Booth, A. and Doolittle, W.F. (2015) Eukaryogenesis, how special really? Proc. Natl. Acad. Sci. (USA) Published online before print April 16, 2015 [doi: 10.1073/pnas.1421376112]

29 comments :

  1. I had never heard the term "eukaryogenesis" before. It seems more pretentious than most scientific terms, especially for an event that almost certainly wouldn't have been a single event at all.

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  2. Awesome paper, I read it yesterday,

    I guess I am guilty of some of those missteps myself, including in print, but their target is the people guilty in eukaryocentrism, a sin I have not committed :)

    Exhaustive characterization of the extant diversity of forms and mechanisms will be key to resolving these issue to the extent they can be resolved. Hopefully there will be funding for that kind of work in the future...

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  3. I have only had the chance to give the paper a quick look. They write:

    "That mildly deleterious traits, some contributing to genomic
    complexity, can be more readily fixed in smaller populations is a
    prediction of population genetic theory (54). Moreover, Lynch
    and his colleagues, as well as one of us, have described ratchet-like
    processes that can create elaborate cellular machinery without
    improving organismal fitness (55)"

    It has always seemed to me that rachet like processes were important in establishing increasing complexity in biological systems. This is why Gould was wrong in arguing that there was no direction in evolution. There is overall a tendency for ever more complex organisms to evolve. This is similar to cosmology where ever more complex structures evolve with time. Plasma, atoms, molecules, stars, galaxies and the Large Scale Structure of the Universe in that sequence.

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    1. It has always seemed to me that rachet like processes were important in establishing increasing complexity in biological systems. This is why Gould was wrong in arguing that there was no direction in evolution. There is overall a tendency for ever more complex organisms to evolve.

      It's not quite correct that Gould found no direction to evolution. He likened speciation to a bush growing against a wall. Organisms could evolve to become more or less complex (think of parasites, cave creatures losing organs or capabilities) or "laterally" in terms of complexity, but up against the "wall," i.e., not-life, the simpler prokaryotes could not evolve to become more simple. Thus the appearance of a direction, while the vast majority of evolution is likely prokaryotes evolving essentially laterally.

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    2. Read Full House in order to understand Gould's arguments about trends.

      Driven trends correspond to the traditional view of an overall movement achieved because each element evolves with a bias for change in this direction. A driven trend to complexity would arise because evolution favors the more complex creatures—and each species of a lineage therefore tends to change in this manner. (In other words, natural selection acts as a driver, conveying each vehicle in a favored direction.) Passive trends conform to the unfamiliar model, championed for complexity in this book, of overall results arising as incidental consequences, with no favored direction for individual species. ([Dan} McShea calls such a trend passive because no driver conducts and species along a preferred pathway. The general trend will arise even when the evolution of each species conforms to a "drunkard's walk" of random motion.) For passive trends in complexity, McShea proposes the same set of constraints that I have advocate throughout this book: ancestral beginnings at the left wall of minimal complexity, with only one direction open to novelty in subsequent evolution. p. 204

      This is the age of bacteria and it will always be the age of bacteria. Complex organisms represent only a tiny percentage of all the organisms on Earth whether you measure it by individuals or total mass.

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    3. No, actually read McShea and more recent work on driven vs. passive trends and in particular the methods by which we can differentiate between them (I've tried to convince some molecular biologists that we should spply them to genome size variation. There's obviously a lower boundary to genome size - even without quibbling about what percentage of the genome is functional, surely genomes are at least of non-negative length. That means we could look at genome size variation using a passive null and check whether we can reject that. Not an idea that was positively recieved, but I think I'll keep trying).

      The ratcheting effect is something at the heart of much of Goulds work, in particular his discussion of von Baers law in Ontogeny and Phylogeny. It's also arguably what's at the core of the Cambrian explosion. In general we have traits that are malleable by evolution and then freeze, because a number of other traits latch onto them, making it harder to modify the original trait without messing with the additions. That's how the genetic code froze. That's why we had more variability in bauplan traits in the Cambrian. That's why we do have apomorphies in the first place - some novel traits strick around as other structures depend on them. You go to an Urarthorpod and sure, the number of segments is going to be variable. You go to modern Beetles and there are Elytra on the mesathorax and flying wings on the metathorax and if you change the number of thoracal segments you are going to mess with that (and all the internal anatomy that goes with it as well). Evolution does have a direction in the sense that crown groups have more derrived character states than stem groups. But that's not something to write home about, because it's trivially true - ancestral organisms had ancestral character states.
      But that's not a trend in the sense we are discussing (it's not even a passive one). A trend is a change in the mean of some particular measurable trait. And that trend is passive if that change can be explained either by neutral evolution in all members of the clade you are looking at. Or if there is selection, but the direction is not constant among clade members.

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    4. Interestingly it was reading that very passage from Gould's "Full House" that Larry quotes that set me off thinking about the importance of complexity rachets. It is not trivial that there is a tendency for an ever increasing highest level of complexity in organisms. It is also parallel to a similar direction observed in the Universe as a whole. For example see Sean Carroll's Emperor Has No Clothes Award Acceptance Speech:
      https://www.youtube.com/watch?v=40eiycH077A at FFRF.

      Which means we have to take thermodynamics into account as a driving force.

      Even in bacteria there has been increasing upper levels of complexity over time, the bacterial and archaeal flagella for example. Idiots may see it's complexity as irreducible however ultimately flagellated micro-organisms have evolved from non-flagellated micro-organism in the distant past through some form of complexity rachet.

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  4. Very interesting article. I suspect that creationists will latch on to the "story telling" comments and ignore the message that the origin of eukaryotes was much less revolutionary and more evolutionary (i.e. step by step) than many biologists think.

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    1. Oh, yes. That opening paragraph is a mother lode for the quote-miners. Bets on how long before UD picks up on it?

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  5. A very interesting read that paper, but I do have to note besides it's more logic and scientific-based arguments (I like the whole thing about questioning the rarity of eukaryogenesis by contrasting it with for example cyanobacteria and so on), that it seems to take issue with what is effectively just personal opinion about a thing's importance.

    How do you question opinion? If a writer says he thinks the origin of eukaryotes was the most important event in the history of life because he himself is a eukaryote, what's the point about trying to undermine that? And how can you even do that other than offer your own opinion about some other related statements of fact? That's one of those debate points you can't ever settle because whatever you may think about something is based on your own, well, opinion.

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  6. I find this interesting because eukaryotes are one of the top examples presented by the contingency side in debates over contingency versus convergence: it happened only once, it must be terribly difficult to achieve, most other planets with life will probably only have prokaryotes, etc. This has never convinced me, mostly for two unrelated reasons:

    First, endosymbiosis events are a dime a dozen. Second, although I must admit that I don't have experimental data or anything, most of the cases where something happened only once in evolution look very much as if the first one to move into that morphospace distorted the fitness landscape so that nobody else can get there any more (because intermediates can't compete well with those who have already got it 'right').

    Think of the land plants. Happened only once and needed a lot of adaptations to get it 'right': cuticule, erect growth, reproductive structures that work in the air, etc. The next alga to try it will be hopelessly inept in comparison - but if the land plants weren't already there, that would not be an issue. I wonder if being a eukaryote is similar.

    So I guess I am biased, but to me this paper fits well into my convergence-ist world view.

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    1. Prokaryote-prokaryote endosymbiosis is extremely rare. There is the nested Tremblaya/Moranella endosymbiont example and another one of an intramitochondrial bacteria, and that's all I can think of at the moment. And there is to this day not a single example of prokaryote-prokaryote endosymbiosis where the host is archaeal.

      Endosymbiosis with eukaryote hosts is indeed rampant, but that's irrelevant - that's after phagocyotsis and all other eukaryotic features have evolved. It's in fact surprising that plastids are monophyletic, given the existence of Paulinella, and that secondary endosymbiosis has probably occured only twice outside of dinoflagellates (and for some reason there seems to be nothing normal about dinoflagellates so no comparisons involving those are fair).

      The argument that the niche was closed does not really work because such an endosymbiont today would not necessarily compete with eukaryotes, thus nothing prevents it from arising, but we haven't seen it yet.

      The way I read it, the main points about the uniqueness of eukaryogenesis that are made in the paper are the distinction between FECA and LECA, the blurred in recent years distinction between endosymbionts and organelles, and that we should not be looking at life from an eukaryocentric (which is just a relaxed anthropocentric) perspective. But they still say the following:

      The combinatorial stringing together of all of the steps between LECA and Macropus rufus (the red kangaroo), Trichomonas vaginalis, or Mozart is, indeed, laughably improbable. Surely, if life’s tape was rewound, none of these would recur (28). However, combinatorial improbability is how evolution works: that eukaryotes arose is not unique in its uniqueness.

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    2. But the argument that the red kangaroo and Mozart specifically are vanishingly unlikely is a creationist fallacy, and usually easily recognised as such. Of course they are - specifically. But nobody really claims that rewinding the tape would again produce Kangaroos - the question is whether it would produce Kangaroo-sized land-living herbivores with an internal skeleton or whether there would be a world with floating balloon animals and walking plants.

      My, and I presume most convergence-ists', view is that because (1) there is a sharply limited number of things that actually work (e.g. walking trees are presumably energetically impossible) and (2) a neglected opportunity or niche will be filled sooner or later (give or take 200 million years I guess), it is probable that rewinding the tape or looking at life on a planet similar to ours would show familiar looking life forms: plants with flat photosynthetic organs, animals with bilateral symmetrcy, an exo- or an endoskeleton, legs, sense organs etc.

      Likewise, when you have three billion years to play around, surely somebody will sooner or later hit upon phagocytosis?

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    3. Georgi, And there is to this day not a single example of prokaryote-prokaryote endosymbiosis where the host is archaeal.

      Not endosymbiosis, and possibly not even symbiosis properly understood, but the relationship here is close enough for extensive gene exchange, in a relationship driven by ATP export (in this instance, from larger to smaller): http://genomebiology.com/2008/9/11/r158

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  7. "They point out that many of the stories about this event are not grounded in fact."

    Many? That is an understatement of a century or may very well be of a millennium. The theory is based on endosymbiosis that is one of the most ridicules and embarrassing theories in biology and possibly all of the science, only second next to the origins of life. People who believe it should be locked up in mental institutions. There is no alternative

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    1. However, you don't actually know anything about endosymbiosis, do you Pest. It's an unfortunate and predictable limitation.

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    2. Do you? Look at SRM how he scrambles NOW to answer the very difficult issue of genes that MUST HAVE COME FROM SPACE for endosymbiosis to take place. Poor evolutionists. They are so confused about their own believes.

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    3. I assumed it is the same Doolittle who wrote a paper few years back and destroyed the Darwin's tree of life and the evolutionary origins of eukaryotes because endosymbiosis was proven impossible to happen from any logical point of view.

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    4. Space genes? Doolittle discussing the non-uniqueness of a transition he previously proved impossible? References, please.

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    5. One gets the impression he knows nothing, and misconstrues and improperly conflates everything he has ever read or heard.

      I imagine I know where he has picked up the space gene notion. But he doesnt understand that the origin of life, evolution, horizontal gene transfer or endosymbiosis doesn't depend upon whether life originally emerged on earth, or was perhaps seeded from an extraterrestial source (as some, including Dawkins,have mentioned as a mere possibility). Pest isn't cut out for thinking much, he needs a new hobby.

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    6. I referred to the article a Doolittle wrote about the tree of life few years back, where he referred to endosymbios as a " fluke" with genes that came from nowhere or as some would put it- from space.

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    7. Actual references would still be better. You've already backed off from the 'space' assertion. There are numerous mechanisms by which genes can seem to have appeared and disappear when comparing modern genomes, and a simple google of Doolitle and 'fluke' returns only hits relating to Doolittle's references to ... flukes (the parasitic flatworms)!

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    8. Maybe Doolittle says the flukes came from space... but we might have to read between his lines to get this meaning, as Pest seems to do.

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  8. This is the age of bacteria and it will always be the age of bacteria. Complex organisms represent only a tiny percentage of all the organisms on Earth whether you measure it by individuals or total mass.

    It's not a novel observation of course, but I'm going to use this specific quote in my courses, whether you like it or not ;)

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    1. I'm paraphrasing Gould. You might want to use his quote instead.

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  9. This does have implications for SETI. One can believe niches get filled, but there may be events that are unique or nearly so.

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    1. The fact that there is even the concept of the Fermi Paradox implies an almost religious belief that the right-most numbers in the Drake equation must not be so small.

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    2. Yes, nearly unique or not, judging from the only experience we have, its taken 3-4 billion years of molecular evolution to produce one measly entity that can purposefully send or receive messages... and that capability arising only in the last 0.0000001 % of that time frame!

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