Wednesday, August 26, 2015

Eukaryotic genes come from alphaproteobacteria, cynaobacteria, and two groups of Archaea

Bill Martin and a group of collaborators from several countries have analyzed gene trees from a wide variety of species (Ku et al., 2015). They looked at the phylogenies of 2500 different genes with representatives in both prokaryotes and eukaryotes.

The goal of this massive project was to find out if you could construct reliable consensus trees of prokaryotes and eukaryotes given that lateral gene transfer (LGT)1 is so common.

The results show that LGT is very common in prokaryotes making it quite difficult to identify the evolutionary history of prokaryotic groups based on just a small number of gene trees.

In contrast, eukaryotes appear to be a monophyletic group where all living eukaryotes are descendants of a single ancestral species. There's very little LGT in eukaryotic lineages apart from one major event in algae and plants (see below).

The genes currently found in eukaryotic genomes show that eukaryotes arose from an endosymbiotic event where a primitive alphabacterium fused with a primitive archaebacterium. The remnant of the alphaproteobacterium genome are still present in mitochondria but the majority of the bacterial genes have merged with archaebacterial genes in the nuclear chromosomes. Thus, eukaryotes are hybrids formed from two distantly related prokaryotic species.

A second round of new genes was acquired in eukaryotes when a primitve single-cell species merged with a species of cyanobacterium. The remnant of the cyanobactrial genome is found in chloroplasts but, like the case with alphaproteobacteria, the majority of the cyanobacterial genes merged with other genes in the nuclear genome.

The exact number of trees was 2,585. Among those trees, 49% of eukaryotic genes cluster with proteobacteria, 38% derive from cynaobacterial ancestors, and only 13% come from the archaebacterial ancestor. Thus, it's fair to say that the dominant ancestor of eukaryotes, in terms of genetic contribution, is bacterial, not archaeal.

One of the authors on the paper is James O. McInerney of the National University of Ireland, in Maynooth, County Kildare, Ireland. He made a short video that explains the result.2



1. Also known as horizontal gene transfer (HGT).

2. I hate to contaminate a scientific post by referring to creationists but I can't help but wonder how they explain this data. I'd love it if some Intelligent Design Creationist could describe how this fits in with their understanding of the history of life.

Ku, C., Nelson-Sathi, S., Roettger, M., Sousa, F.L., Lockhart, P.J., Bryant, D., Hazkani-Covo, E., McInerney, J.O., Landan, G., Martin, W.F. (2015) Endosymbiotic origin and differential loss of eukaryotic genes. Nature Published online Aug. 19, 2015 [doi: 10.1038/nature14963]

55 comments :

  1. The exact number of trees was 2,585. Among those trees, 49% of eukaryotic genes cluster with proteobacteria, 38% derive from cynaobacterial ancestors, and only 13% come from the archaebacterial ancestor. Thus, it's fair to say that the dominant ancestor of eukaryotes, in terms of genetic contribution, is bacterial, not archaeal.

    If and only if you think shared gene content is equal to phylogeny. This idea kind of fell out of favor a decade ago when people made trees of gene presence/absence and saw that most endosymbiotic bacteria clustered together -- because they lost more or less the same genes.

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  2. Nice piece Larry. I'm proud to say that James McInerney is now a colleague at the University of Manchester in the UK... If only we could get Bill Martin and Nick Lane, too!

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  3. Not unlike what happened to English in the early Middle Ages. As Norse and French-speaking populations became absorbed by the English-speaking majority, their vocabularies contributed to the lexicon of Middle English. English, the host language, is phylogenetically Germanic, and the vast majority of frequently used, "essential" words are vertically inherited from Old English (many of them can be traced back to Proto-Germanic and Proto-Indo-European). Still, words of Romance origin clearly outnumber all the other components of the modern lexicon, and you can hardly build a sentence without using a few of them.

    For example, in the highlighted clause above, the following elements are Germanic:

    words, of (twice), -ly, out-, all, the (twice), other;

    these are Romance/Latinate:

    Romance, origin, clear-, -number, components, modern;

    ... and there's a sole instance of horizontal transfer from scholarly Greek:

    lexicon.

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    1. But what about Celtic components? Like -ing.

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    2. -ing is not a Celtic component. But of course there are British Celtic loans in English, and Continental Celtic loans borrowed before the ancestors of the Anglo-Saxons settled in Great Britain, and loanwords from scores of other languages. It's only a loose analogy anyway. Languages in general behave more like prokaryotes as regards lateral transfer: there's a lot of it.

      I drew the analogy between the eukaryotic genome and the chimaeric lexicon of English because it extends to the functional role of genes and words. The "housekeeping" function words, responsible for expressing grammatical relations and laying out the structure of the sentence, are almost without exception "native" (retained from the host language). But most content words (the building blocks) are foreign and acquired either by ordinary sporadic borrowing, of by the kind of mass influx that came in the wake of the Norman Conquest. Vertically inherited words outnumber loans only in the most frequently used "core vocabulary". A word which people hear frequently and have to use hundreds of times a day is more "essential" for communication and (statistically) more resistant to replacement than a rarer one which you may use to express a nuance of meaning a few times a year.

      To quote from Ku & al.

      Block D encompasses genes that were present in the eukaryotic ancestor, that are very densely distributed in archaea, and that are also more refractory to loss than any other group of eukaryotic genes. These correspond to the informational genes[32] representing the archaeal host lineage that acquired the mitochondrion in endosymbiotic theory[34, 35, 36]. The archaeal genes in eukaryotes are rarely lost (Fig. 1), being more essential than operational genes37 and involved in information processing: unlike genes in metabolic pathways, their function cannot be replaced by importing amino acids or vitamins from the environment[29, 38].

      I see an analogy here, and I find it interesting for my own discipline.

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    3. @Piotr

      All of those Romance/Latinate words have counterparts in several other Germanic languages, so are you sure these words were brought into the English language by the French? Perhaps they were adopted independently into languages like English and German? Or did they spread around later, when English got some widespread use (that's pretty late, I think).

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    4. Clear and number came with the Normans (though of course they too have counterparts elsewhere in Germanic because of independent borrowing). Sometimes their separate histories can be seen in their form. For example, German klaar came from Latin clarus rather than via French, since it doesn't show the telltale change of the vowel (a > e) which gave Old French cler (borrowed into Middle English in the same form).

      I didn't mean to imply that all the words in my example are of Medieval origin. Contacts with Anglo-Norman led to a partial re-lexification of English with French elements, leaving the door wide open for massive borrowing from mainstream literary French in the 14th century and later, when the Anglo-Norman population had already been absorbed by English society. If you want actual examples of words of Anglo-Norman origin, they are often quite humble everyday items like very, people, aunt, use, chair, pork, crown, story etc. -- nothing recherché. They have assimilated so successfully that people list some of them when asked to give examples of "good Anglo-Saxon words". Then there are words borrowed to and fro, like war, which in English is a loanword from Norman French (corresponding to Central French guerre), but in French represents the Germanic lexicon contributed by the Franks.

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    5. @Piotr

      Fascinating stuff!!! I had to remerge from lurk-mode to follow up on Corneel's line of inquiry given I am just a few km from Kassel the birthplace of Gebrueder Grimm

      How exactly can linguists distinguish between vertical from horizontal transfer when all cognates are similar to the presumed original IndoEuropean root.

      I liken what I am attempting to articulate as "saying" the same word with either a Germanic or Latinate or even a Slavonic "accent" which will generate results that may appear to be horizontal borrowing when in fact they represent vertical inheritance.

      Of course, linguists must have developed methodologies for distinguishing one scenario from the other; I just would like to know in more detail what these would be.

      Thanks in advance

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    6. How exactly can linguists distinguish between vertical from horizontal transfer when all cognates are similar to the presumed original IndoEuropean root.

      Vertical transfer leaves some indelible marks -- regular sound changes which are only found in a particular lineage. If a word displays them, they are evidence that it spent part of its history together with other structurally similar words in a language in which such characteristic modifications were applied. Borrowed words skip at least some of them. Jacob Grimm was the first linguist who discovered the systematic character of sound changes (this is why the most conspicuous synapomorphy defining the Germanic group is called Grimm's Law).

      For example, the words brother and fraternal are related, but even if it weren't obvious that the latter is a Latin loan, the pattern of consonants would tell us which of them is vertically descended via Proto-Germanic: brother contains two instances of Grimm's Law, shows the regular Germanic development of the stressed vowel, and regularly corresponds to related family terms in Sanskrit, Latin, Russian, Irish, etc. The most parsimonious conclusion is that it's always been part of English, Germanic, and Indo-European vocabulary. Terms for the nuclear family members are typically "highly conserved" across languages (though not without exception, see the Ancient Greek neologism adelphós which took over the original meaning of the inherited Indo-European word phrā́tēr; the latter survived in a marginal function, as 'clansman, community member').

      By contrast, fraternal shows some characteristically Latin (or more generally Itallic) features, e.g. the treatment of the initial consonant, reconstructed as Proto-Indo-European *bh in the 'brother' word (which regularly became *f in Italic, including Latin). It also retains the original stop pronunciation of PIE *t, which should have changed into a fricative in Germanic (as a result of Grimm's Law). This shows that at the time when the law was active in Germanic, the ancestor of the word fraternal was somewhere else (to wit, in Old Latin). It made its first documented appearence in English in the mid-15th century (borrowed from Medieval Latin).

      Now if you look at French, the regular vertical descendant of Latin frater in that language is frère. One characteristic thing that happened here in the passage from provincial Latin to French was the vocalisation of the medial /t/ resulkting in its complete loss (since it was regular, it happened also in père, mère and lots of other inherited words). It follows that French fraternel, though related to frère, is not part of the inherited Latin lexicon (or it would not have skipped the loss of /t/, not to mention the fronting of the root vowel to /e/, which is also regular in French). It is a learned word borrowed from Latin (written school Latin, as opposed to the spoken language of Roman Gaul), probably about the 12th century, too late to be affected by the diagnostically Gallo-Romance changes.

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    7. I see an analogy here, and I find it interesting for my own discipline.

      Careful, lest linguistics blogs start to be haunted by "Tower of Babel-ists." ;-)

      For amateurs interested in linguistics, any blog and book suggestions?

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    8. @Piotr
      "Languages in general behave more like prokaryotes as regards lateral transfer: there's a lot of it"

      Just like issues of false cognates are used to make absurd claims (English "sheriff" is not a transfer from Arabic "sharif" despite dubious claims, etc.), you meed to be wary of claims of horizontal gene transfer. HGT should be the absolute *last* explanation in incongruent phylogenies rather than the first as it all too often is.

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    9. My all-time favourite book for people interested in language change and related topics is Larry Trask's Historical Linguistics. The author's didactic and writing skills make it a pleasure to read even if the stuff gets difficult in some chapters. Larry Trask (an American who got his PhD in London and settled in Sussex) died in 2004 and is greatly missed not only by colleagues world-wide but also by his Internet fans (he was very active on several discussion lists). A new revised edition of his book (in fact revidsed so much that Robert McColl Millar must be treated as its co-author) has just been published by Rutledge. It has a nice accompanying website

      One blog regularly haunted by some of the best linguists is this:

      Language Log

      Strongly recommended.



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    10. you [n]eed to be wary of claims of horizontal gene transfer. HGT should be the absolute *last* explanation in incongruent phylogenies rather than the first as it all too often is.

      I'm aware of that. Of course no linguist would claim that sheriff is an Arabic loan (accidental similarity between unrelated words is much more probable than most people imagine), but the danger you mention is quite real. There are, for example, many "de novo" words, often just fancifully coined by someone and picked up by others. Most are restricted to slangy registers and die out quickly after a brief burst of popularity, but some manage to invade mainstream vocabulary and get a secure position there. A few hundred years later etymologists scratch their heads, wondering what to make of words of "unknown origin". There is a whole school of "substrate" enthusiasts (professional linguists, not Internet kooks) who posit otherwise unattested extinct languages to account for the words they can't etymologise. This is of course a case of obscurum per obscurius. I don't mean that those people can't be right; occasionally their arguments deserve serious attention. But lateral transfer from an unidentifiable source is the really really last thing one ought to propose.

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    11. Larry Trask ... is greatly missed not only by colleagues world-wide but also by his Internet fans (he was very active on several discussion lists).

      Very active, and very willing to explain things to people not expert in linguistics. He didn't hide his contempt for Merritt Ruhlen or people who said ignorant things about Basque, but otherwise he was courtesy and kindness itself. sci.lang has gone steadily downhill since he died (still quite young).

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    12. I am reminded of a particularly insightful analysis of lautverschiebung in the English language

      http://www.comedycorner.org/45.html

      ;-)

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  4. This comment has been removed by a blog administrator.

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    1. He's told you he won't remove anything that contributes to the discussion. The criterion is not whether you agree with him; it's whether you have anything to say. Hint: that post is not long for the world.

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  5. This research is explained (from a creationist standpoint) as a glimpse of pre-fall symbiotic relationships. Of course, things are clearly different now. Those once beneficial relationships are often no such thing, and in some cases are parasitic.

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    1. Who (and I mean some specific person) explains it that way?

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    2. My reply was a response to Dr Moran's footnote (2), in which he invited creationist explanations. I'm afraid I didn't find that given (at least in the video) very satisfying (though I accept many will say the same about mine). I'm not speaking on behalf of anyone else. Other creationists might have different explanations, or they might agree with the view presented.

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    3. So, if I'm understanding you, you are the creationist who explains it that way. Would you care to engage in a scientific discussion of your interesting hypothesis?

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    4. a glimpse of pre-fall symbiotic relationships

      and after the 'fall", then what? And what exactly is this fall? Nevermind.

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    5. Adam had no mitochondria before the Fall? I'd suggest he was a bit sluggish, then. And the Tree a bit on the pale side.

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    6. But archaea lay down with proteobacteria, and cyanobacteria dwelt with them both.

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    7. I'm afraid I didn't find that given (at least in the video) very satisfying (though I accept many will say the same about mine).

      Fair enough. So perhaps you could provide a citation to the peer-reviewed scientific study that refutes the evidence in McInerney's paper, and which instead demonstrates that "the fall" explains these findings. You neglected to include that in your initial post, but I'm sure that was just an oversight on your part.

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  6. Larry, my creationistic ears picked up on something fascinating at 1:30:

    To paraphrase James McInerney ..."the dominant means of evolution is losing genes from the ancestral genes or perhaps making their own genes through some other means...

    The former sounds so very Behe-esque and the latter sounds oh so design-esque.

    Curious if any of the regulars actually listened to the clip, and why didn't they pick up on this and attack him for his closet-creationism.

    This is just scandalous!!!!!!!!!! Scandalous, I say!!!!!!!!!

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    1. Profesor McInerney can't be blamed for the fact that an IDiot quotemines him and reads an IDiotic interpretation into his words.

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    2. Then do tell Piotr what, in the context of his comments does "the dominant means of evolution is losing genes from the ancestral genes or perhaps making their own genes through some other means..."

      Lets watch you parse this one in evolution-speak.

      Its always co-opting designed objects then denying them in the same breath.

      Have you no shame??!!

      Guess its the "Reverse Dunning-Kruger Effect" in action again.

      Your superior experience, skills, and intellect prevent you from detecting, but more so admitting the most basic contradictions in your logic.

      Piotr: Man is intelligent, but nature is not. Man designs, but nature does not.

      Why? Is it because Man is not a product of nature?

      Ah, that's it!! So Man IS God !!

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    3. He obviously means that eukaryotes started losing the ancestral bacterial genes because lateral gene transfer is very rare in eukaryotes, so as eukaryotes evolved in their own lineages, their DNA started diverging from bacterial DNA

      You are fucking retarded

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    4. Steve, you are an excitable chap. If there is no HGT, a lineage only has loss or change available to it.

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    5. Well, magical creation of new genes nothing by God is also another theoretical option. But I didn't hear McInerney mention anything about that. Steve seems to think he did, however. Maybe Steve needs new speakers on his computer.

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    6. First off, Steve, you lifted his words out of their context. McInerney wasn't speaking of evolution in general, but was talking about eukaryotes, contrasting them with prokaryotes. Prokaryotes often acquire new genes from other prokaryotes via HGT. Eukaryotes don't, so their evolution has consisted mainly in losing some of the genes inherited from their archaeal and bacterial ancestors, while at the same time well-known natural mechanisms (as opposed to a supernatural Designer) have been giving rise to lineage-specific genetic novelties (including new genes). If a lineage loses one of the ancestral genes, it cannot be replaced by lateral transfer from a different species, so the absence of the ancestral gene is transmitted along the branches of the family tree. Thus, both losses and gains confirm that eukaryotes do form a rather neat family tree, with clades nested within clades. Neither the Unflappable Behe nor God have anything to do with this business. Yeah, I know Behe accepts common descent and Ga timescales of evolution, but that makes him similar to mainstream biologists (in these respects), not vice versa.

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  7. James McInerney talks about mitochondria and chloroplasts having clear bacterial origins. Was the origin of mitochondria still in dispute and does this work now make it settled science?
    Does the evidence point to this being a singular event in the evolution of life?

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    1. I think it's been well-supported for a while. This is a broadening out of the analysis.

      It's not clear whether an endosymbiosis happens once only, or whether the conditions that lead to the first association are sufficient to allow it to happen between the same species multiple times. There are interesting examples of serial endosymbiosis, russian-doll style.

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  8. "In contrast, eukaryotes appear to be a monophyletic group where all living eukaryotes are descendants of a single ancestral species. "

    And what a magical feat that would be for that Mr. Eukaryotic Ancestor.

    The Shine-Dalgarno sequences for all the prokaryotic genes in that Mr. E Ancestor simultaneously in almost all gene loci convert to Kozak sequences and then the spliceosomal introns get inserted into all the prokaryotic genes to make them look like eukaryotic genes. Not to mention the machinery to implement spliceosomal introns comes into place in a way that's darn near perfect from the start lest the snipping out of exons goes awry and kills the organism.

    This surely isn't a transformation that happens gradually at the population level. Do we have creatures with half their genes looking like prokaryotes and half like eukaryotes and then they evolve fully into eukaryotes? Did we have some warm little pond where the prokaryotes gradually transformed their genes to have eukaryotic exons along with Kozak sequences instead of Shine-Dalgarno sequences? And lest we forget, histones were in Mr. Eukaryotic Ancestors, maybe some Archaea, but mysteriously missing from bacteria. That's just Fenomenal with a capital "F".

    So how did Mr. Eukaryote Ancestor evolve. How many Fs are in the word "way"?


    The macro evolutionary step from bacteria to eukarya is so extraordinary it is hardly distinguishable from an act of special creation.

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    1. it is hardly distinguishable from an act of special creation

      Don't you realise how pathetic you guys look when you use your own religion's central tenets to mock evolution or atheism?

      Like the classic "takes more faith than christianity"

      Screams inferiority complex

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    2. liars,

      Why do you abuse science in this manner? You learn enough superficial knowledge of science so you can use some sciencey sounding jargon, and create a caricature of some scientific concept to knock down, and enter each new discussion thread pretending you are making these arguments for the first time.

      Anyone with a good understanding of these concepts sees your preposterous arguments for the straw men they are. What's worse than that, is that you don't even care. You'll fool some gullible people who know less than you about the science and want to keep believing in the religious dogma of creationism. liar, indeed.

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  9. Chris B,

    I refer the reader to this tacit admission of the problems I raised:

    http://www.biologydirect.com/content/7/1/11

    "The elucidation of the general scenario of evolution of eukaryote gene architecture by no account implies that the main problems in the study of intron evolution and function have been solved. Quite the contrary, fundamental questions remains wide open."

    My argument was not preposterous. What is preposterous is the idea a cell gets 80% of its genome suddenly invaded by intron inserting parasites that shred its genes to pieces and somehow spliceosomal mechanism poofs out of nowhere at the very same time in order to rescue the poor critter from disaster. That's about as far fetched as a magical "poof" and hence is no less fantastic than a miracle. Evolutionary biologists unwittingly appeal to miracles, they just don't admit it.

    "What are the mechanisms of intron loss and gain? There is very little direct evidence of any. A consensus seems to exist regarding the role of reverse transcription in intron loss although even this mechanism badly needs experimental corroboration. As for the mechanisms of intron gain, indications of the involvement of double-strand break repair notwithstanding, the study of this key problem has not even started in earnest. "

    You're the one being gullible in this debate if you swallow the idea that phylogenetic reconstructions actually prove the mechanical feasibility of evolution, it doesn't. Phylogenetic reconstructions are nothing more than looking at patterns of similarity then concocting fanciful telling stories that give no considerations to the feasibility of those stories from a mechanical stand point. If they did give serious consideration, evolutionists would admit they are basically invoking miracles in order for evolution to work.

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    1. My argument was not preposterous. What is preposterous is the idea a cell gets 80% of its genome suddenly invaded by intron inserting parasites that shred its genes to pieces and somehow spliceosomal mechanism poofs out of nowhere at the very same time in order to rescue the poor critter from disaster. That's about as far fetched as a magical "poof" and hence is no less fantastic than a miracle. Evolutionary biologists unwittingly appeal to miracles, they just don't admit it.

      This is not at all what the scenario is.

      What most likely happened is that the alphaproteobacterial endosymbiont brought some group II introns with it, which then invaded the archaeal host and proliferated in it (why that is is a mystery, but there is still only a single example of a group II intron in archaea and that is a result of very recent HGT event). Note that these are self-splicing introns so no spliceosome is needed. However, with time, some of them started degenerating and had to rely on trans-activities to be properly spliced out. Here things get really speculative but this is what might have driven the evolution of the nucleus (the need to separate transcription from translation so that to give time to the now much slower process of splicing to finish before translation starts). Then the spliceosome gradually emerged with an snRNA core homologous to the group II introns (the overall structures are still very similar even if it's multiple snRNAs in today's spliceosome) plus some archaeal proteins.

      There is nothing magical about that process.

      The weak point in that scenario is the initial survival of the archaeal host with the large number of group II intron insertions in its genome, We don't know nearly as much about it as we would like. But we know something of the sort must have happened because the LECA was very intron-rich.

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    2. Also note that the modern spliceosome is incredibly complex, but this is the result of some 2 billion years of evolution.

      It certainly wasn't that complex in the beginning, and it certainly need not be that complex to function. There are examples of greatly reduced spliceosomes even in modern organisms (PMID: 25733880)

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    3. No, liar, I am not gullible and your arguments are indeed preposterous.

      "What is preposterous is the idea a cell gets 80% of its genome suddenly invaded by intron inserting parasites that shred its genes to pieces and somehow spliceosomal mechanism poofs out of nowhere at the very same time in order to rescue the poor critter from disaster."

      That indeed would be preposterous, and this is where you are lying to people. You created the straw man scenario where all these things poofed into existence, then you knock it down. Evolutionary theory says nothing of the sort, and you know it. That's just the argument you want to have. Georgi set forth a perfectly plausible scenario but you won't accept it. You know the emergence of eukaryotes is so deep in geologocal time that we can most likely never say for certain exactly how it happened. You try to capitalize on that uncertainty, and hide your god in that gap

      "That's about as far fetched as a magical "poof" and hence is no less fantastic than a miracle. Evolutionary biologists unwittingly appeal to miracles, they just don't admit it."

      No it is the religious dogma of creationism that involves miracles and things poofing into existence. Your alternative is "science can't explain exactly how it happened, so god poofed it into existence.

      "You're the one being gullible in this debate if you swallow the idea that phylogenetic reconstructions actually prove the mechanical feasibility of evolution, it doesn't. Phylogenetic reconstructions are nothing more than looking at patterns of similarity then concocting fanciful telling stories that give no considerations to the feasibility of those stories from a mechanical stand point. If they did give serious consideration, evolutionists would admit they are basically invoking miracles in order for evolution to work."

      More shameless obfuscation from liar. Phylogenetics can't explain the emergence of eukaryotes, so all phylogenetics is just story telling and evolution is all wrong. That irrational nonsense might work on folks at the UD echo chamber, but it won't get you far here. The unknown aspects of eukaryotic evolution do not somehow invalidate the mountains of phylogenetic evidence in favor of evolution.

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    4. There is also the underappreciated phenomenon of the compression of our perception of deep time.

      The more distant some events are in the past (or in the future), the less we appreciated how long it was between them. The Cambrian explosion is a classic example - 510mya, 540mya, 570mya, etc, it's all the same for most people, but in reality we are talking about tens of millions of years.

      It's even worse with eukaryogenesis. We have no fossil record (and will never have one), and we have no idea how much time passed between the establishment of the initial endosymbiosis and LECA. It could have been quite short (as in tens of million of years) but most likely it was hundreds of millions of years (the two classic examples of ongoing organellogenesis, the chromatophores of Paulinella and rhopalodiacean spheroid boides date back to 40-60 mya; note how far exactly the process has gotten in that time). A lot can happen in such a period, especially in a microbial population exploring new niches.

      It was by no means an instantaneous event, it took a long time.

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    6. The Cambrian explosion is a classic example - 510mya, 540mya, 570mya, etc, it's all the same for most people, but in reality we are talking about tens of millions of years.

      Not to mention the cognitive inability to appreciate how utterly long just one million years is in the first place.

      Anyway, it seems to creationists everything is always about complex things "poofing into existence" - it is all they can imagine. In a sense, their beliefs are well-placed because if complex things did poof into existence as they imagine, then surely gods would be required.

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    7. Humans seem to perceive time in terms of reference points, not in terms of actual numbers. That's a major reason why we have a much better perception of the recent past, which is densely filled with familiar reference points, but start to lose grasp of the distant past as the records become sparser, It's true for human history, it's true for deep geological history too.

      Now it's true that most people fail that test too, but let's imagine a moderately educated person, who has not skipped all his history classes and happens to read a book from time to time - he will have a fairly good idea of what went on in the last 200 years. But the time between 700 and 800 mya ago will be a blank for him - those will be just two numbers with no real meaning to him. A geologist will have an analogous, but not nearly as sever problem, as he will know quite a bit more about the more recent past than that particular period, but he would also know about the Snowball Earth, the changes in the geochemistry of the planet, etc., so he would have a much better grasp of the length of the period than the average (moderately educated) person.

      The same applies to creationists - there is the natural human bias toward compression of the past, and on top of that is layered the complete lack of reference points due to the ignorance, illiteracy and stupidity that are core characteristics of the creationist mind. After all, if someone knew a little bit about the geological history of the planet, it is far less likely that he would ever become a creationist (the inverse is true too - being a creationist quite efficiently insulates one from ever learning about such topics). And that's how we end up with people claiming that things just poofed into existence in an instant and that evolution cannot explain that...

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    9. You should read what Georgi wrote, Sceptical Mind, instead of just throwing out an inane challenge.

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  10. "Also note that the modern spliceosome is incredibly complex, but this is the result of some 2 billion years of evolution."

    That was the scenario in the paper referenced as the spliceosome had to acquire its daunting complexity quickly and early on lest the cell die. That's the problem with evolving life-critical features, there has to be lots of simultaneous change, not gradual change.

    And one thing that is known, but rarely acknowledged except by researcher like Stanley Salthey -- the features most likely to evolve are the features under the least selection, since changes life critical features sort of have to be simultaneous rather than gradual.

    "at the mechanistic level, the adaptation of the early eukaryotes to the swarms of genomic parasites (if this is what introns are, Figure 9), which severely compromised the integrity of their genomes, an adaptation that apparently involved rapid evolution of the dauntingly complex spliceosome, remains an intriguing enigma. The intron invasion, probably spawned by the mitochondrial endosymbiont (Figure 9), could have led to a peculiar, intron-dominated genome architecture of the early eukaryotic, with up to 80% of the genomic DNA comprised of introns "

    The 80% happened early, not over billions of years. The spliceosome had to evolve rapidly as well. What you said is in conflict with an accepted paper. That's ok, it's not the first time evolutionists can't agree over unworkable evolutionary scenarios because evolutionary theory needs miracles to make it work, but that is the one thing evolutionary theory will not allow even though it sorely needs it.

    A half-baked spiceosomal implementation will be likely lethal. What if it snips out the wrong pieces in the wrong way. Oh well, that mRNA going to the ribosome is just packed with garbage.

    As the paper acknowledge: "remains an intriguing enigma". Translation, "we don't know how this could happen without a miracle, but we'll keep believing, we'll keep the faith."

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    1. What does the bible say about how it happened? Did god use the rib of some prokaryote maybe? I mean with your amazing knowledge on the subject you could spare scientists so much time and work, you know.

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    2. And once again we see a disastrous failure to understand deep time and the process of evolution. "Quickly" in this context does not mean instantaneous.

      It's extremely unlikely that one day an alphaproteobacteria entered an ancient archaeon, and in the next generation the archaeon had its genome invaded by thousands of group II introns, with which it had to deal with. The only quick (in your understanding of the word) event would be the extinction of such a lineage.

      Look at modern bloated genomes -- they did not end up bloated all of a sudden, they expanded over millions of years. The invasion of the archaeon by introns wasn't instantaneous either, it happened over many generations, the transition from self-splicing to trans-mediated splicing wasn't instantaneous either, and neither was the evolution of the spliceosome. "Quick" on a geologic time scale? Yes. but that does not mean magically poofing into existence. And it does not mean the evolution of a 200-component spliceosome -- it was complex but much less complex than that, and it probably evolved in parallel with the degeneration of the group II introns, meaning that it had to do a less-complicated job than modern spliceosomes. That took time. Not "billions of years" (where the hell did that come from? - nobody is claiming that), but not months either.

      In any case, it is far from a hypothetical scenario that this is what happened.

      First, I mentioned above that the structure that the snRNAs adopt is very similar to that of group II introns even if they are in multiple pieces now, But that is hardly unprecedented -- there are all sorts of examples of proteins that during evolution break up into two separate proteins, which then carry out the same function as part of a complex. And there are also a number of examples of ncRNAs doing the same -- the rRNA is fragmented in a number of organellar genomes but then the pieces still adopt the more or less regular conformation. So that step is hardly unimaginable.

      Second, archaea have Sm proteins, so one of the main components of the spliceosome was already available in the ancestor.

      P.S. Am I the only one noting the deep irony of creationists having to argue against evolution based on which scenario for the evolution of spliceosomal introns and splicing, which happened 1.5-2 billion years ago, is correct?

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    3. Am I the only one noting the deep irony of creationists having to argue against evolution based on which scenario for the evolution of spliceosomal introns and splicing, which happened 1.5-2 billion years ago, is correct?

      Exactly Georgi! That's why I asked him what does the bible say about how it happened.
      He's the one claiming it was some sort of miraculous event, so there must be the hand of gawd behind it, right?
      It's infuriating, they always come up with some "impossible" scenario, then claim that's what scientists actually believe that happened and call them out for it. Doesn't get much more dishonest than that

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    4. I started writing that comment an hour before it was posted, and then got interrupted, so I didn't see yours. But that is exactly how it is indeed.

      Also, one can find many religious leaders and organizations (going back man centuries in fact), warning against the use of god-of-the-gaps arguments. But they never listen even what such people are saying...

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    5. Asking for "replication" is a clear sign of lack of understanding of the evolutionary process. There is no reason to think it will produce the same thing if it was repeated under the same conditions. But it cannot be repeated because the conditions cannot be reproduced.(and aren't even known).

      Also, there is nothing wrong with telling someone that he doesn't understand something if he indeed doesn't

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    6. The prince of darkness will take care of you

      ...and he's finally gone full retard. LMAO

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