447 thoughts on “The Mysteries of Evolution: 6. Endosymbiosis-The second miracle of life after the origin of life”

1. colewd,

   What do you think is the strongest evidence for the origin of mitochondria. The internal structures are very different so even though they have similar shapes I am finding it hard to believe one came from the other.

   I am quite sure you are capable of Googling this. But:

   Cardiolipin and other inner membrane features not shared with main cell but found in bacteria
   Circular DNA
   No introns
   No histone
   Assigned STOP codon
   Their own tRNAs
   Independent reproduction
   Ribosome structure
   Susceptibility to antibiotics
   Oxidative phosphorylation
   Phylogenetic analysis (that thing you don’t believe in)

2. J-Mac,

   So what’s new that you have written since your many previous fruitless comments? You used different words to describe the same?

   My questions have been substantive. You haven’t addressed a single one of them. Remember Wolbachia? Or, what is your alternative explanation? Or, what exactly are the missing genes? Or, why would an experiment convince you of the historical reality of the event? Or, why couldn’t endosymbiosis happen?

   But no, silence or smokescreen. Like many a Creationist, you scuttle off, deeply wounded by some vague slights, distracting from your failures like a squid billowing ink. Touchy bunch.

   Until you come with something worthwhile

   I will if you will.

3. Allan Miller,

   Oh, hang on, I missed one. Hold on to your hats, it’s a doozy … N-formyl methionine! Yes! I know!

   I was just looking at my list, and wondered whether mitochondria and chloroplasts might use the same initiation codon as bacteria. Most proteins begin with the codon AUG, which codes for methionine in nuclear and Archaeal genes, but N-formyl methionine in bacteria. Now, no prizes for guessing what Professor Google tells me codon-1 AUG codes for in chloroplasts and mitochondria …

   I can’t guarantee I didn’t already know this and had forgotten. But it’s still an interesting example of the use of ‘prediction’ in science. If organelles came from bacteria, one would expect them to have features in common with them which are distinct from the rest of the cell. Pick a feature, check. If they aren’t held in common, that doesn’t disprove the hypothesis, but if they do, that’s a strike in its favour.

   The accumulated evidence is what counts, not any one thing, though I’d put fMet at the head of the list as my banker. Phylogenetic evidence is better, but we’ve seen what problems people have, or invent, with that. Often in sentences beginning ‘Just because …’.

4. Allan Miller:
   colewd,

   I am quite sure you are capable of Googling this. But:

   Cardiolipin and other inner membrane features not shared with main cell but found in bacteria
   Circular DNA
   No introns
   No histone
   Assigned STOP codon
   Their own tRNAs
   Independent reproduction
   Ribosome structure
   Susceptibility to antibiotics
   Oxidative phosphorylation
   Phylogenetic analysis (that thing you don’t believe in)

   And more is still being found and the list keeps growing.

   Bacterial tail anchors can target to the mitochondrial outer membrane
   Güleycan Lutfullahoğlu-Bal, Abdurrahman Keskin, Ayşe Bengisu Seferoğlu and Cory D. Dunn
   Biology Direct 2017 12:16
   https://doi.org/10.1186/s13062-017-0187-0

   Background

   During the incorporation of an α-proteobacterial endosymbiont within the eukaryotic cell, genes transferred to the (proto)nucleus were re-targeted to mitochondria, allowing these organelles to remain the location of crucial cellular processes [1, 2, 3]. In addition, other polypeptides that evolved within the eukaryotic lineage or that were acquired through lateral gene transfer from other organisms were directed to mitochondria [4, 5, 6]. Across eukaryotes, the β-barrel Tom40 protein forms a pore by which proteins pass through the OM [7, 8, 9]. However, the Tom40 polypeptide seems to require already existing TOM complexes for mitochondrial insertion [10, 11], giving rise to a “chicken or the egg” dilemma when considering how the TOM complex may have evolved.

   Several narratives might be proposed for how mitochondria first evolved the ability to transport proteins from the cytosol. In one scenario, an early translocation pore that was self-inserting at the mitochondrial surface might have allowed mitochondria to begin to import proteins, permitting the subsequent evolution of the translocon found in eukaryotes today [12]. Current evidence suggests that the self-insertion of tail-anchored proteins at the mitochondrial OM is possible [13, 14, 15], and some tail-anchored pro-apoptotic proteins appear to have the ability to generate membrane pores at mitochondria [16, 17], making tenable such a scenario for the evolution of mitochondrial protein import. At the inception of mitochondria, such tail-anchored proteins would likely have been derived from prokaryotes, particularly if mitochondria were required for the generation of the stereotypical compartmentalized structure of eukaryotes.

   We focused our attention upon a single aspect of this hypothesis: can TAs obtained from bacterial proteins be inserted into the mitochondrial OM when expressed within a eukaryotic cell? Indeed, our results demonstrate insertion and function at the mitochondrial OM for predicted TAs encoded by the proteobacterium E. coli, and we describe the relevance of our findings to the concept of lateral gene transfer during eukaryogenesis.

5. Allan Miller,

   No introns

   I’m going to withdraw this simplistic statement. There are, for example, self-splicing Group I introns in plastids and bacteria. There are none in Archaea AFAIK. But, one would have to be careful about assigning too much significance to this pattern. It’s not clear whether they went extinct in Archaea, or were never present. Nor can one be sure that their presence in nuclear genes indicates inheritance from the Archaeon (which would have to be prior to extinction, if that’s what happened) or gene transfer from organelles. Nonetheless – regardless of the directions of travel – it’s a curiosity that endosymbiosis would clear up nicely either way. There’s no clear functional reason for the pattern.

6. Rumraket,

   From paper: Several narratives might be proposed for how mitochondria first evolved the ability to transport proteins from the cytosol.

   Yep – I quite like the possibility that it started as ectosymbiosis too, though. The Ignicoccus/Nanoarchaeon system I mentioned earlier has inter-cell transport which seems readily adjustable to a 2-membrane interior system.

7. By the way, this gibberish is very confused:

   stcordova: Regarding for example the Intiation Factors, they either connect to the complex in some particular order or they don’t. Those are discrete components and in discrete spatial positions. At the chemical nano-level things are either their or not. It’s not like something like body weight that can undergo gradual transition. Because of that discrete quality, transitions from a supposed ancestor will be fraught with the problem of having dead transitionals along the way because simultanoues changes are needed.

   At the miscroscopic level of atoms and molecules, there really is such a thing as varying degrees of association between individual components. Both in terms of how strongly they associate, and how this association changes gradually over time.

   This “lego” idea you’ve apparently got in your head is simply not correct. Binding strength can be anywhere in between nonexistant (there is no association), to inseperable(they’ve become covalently linked together). And can be highly sensitive to things like temperature and pH. These facts are routinely exploited both by the biochemistry of life, and in molecular biology techniques employed in the laboratory. A simple example is PCR where annealing and melting temperatures for primer-template and template-template are critical to what kinds of products you get (if any).

   Some molecules can loosely associate with the surfaces of other molecules and sort of bounce around on their surface under brownian motion, without ever really attaching in some particular spot.

   Here’s a PCR temperature gradient I ran about a year ago to find the optimal annealing temperature for a primer designed to target only a single specific locus (about 700 basepairs) in a small section of the human genome, marked by a green arrow. From left to right, the temperature increases by half a degree between A and B, B and C etc. This is for a roughly 20 bp primer. Notice the large difference in quality between the C and D lane. Half a degree centigrade and suddenly you get a lot of nonspecific binding for that 20 bp DNA piece. The optimal temperature would be somewhere in between the D and E lane, so we are talking a quater of a degree change. Notice the thickness and intensity of the bands between each lane. It changes, meaning the degree of association between primer and template changes.

8. J-Mac,

   It just further proves my points in this OP and above…I guess I should cry now? Is that what you were expecting me to do??? It is very shocking and sad…

   What I expected you to do is exactly what you’ve done. I provided evidence that demonstrated that your claim that the theory of evolution is dead is false. And that in fact the evidence is that your preferred explanation is dead. ID is moribund.

   And did you acknowledge or dispute that? No. You just claimed it proves your points made in the OP. Without naming them or demonstrating how, I would note.

   So, just like Sal, you pick and choose and ignore what does not support your argument. It’s ok. It’s what I expect from your average creationist.

9. J-Mac: If you have decided to resort to personal attacks on me this tells me you came to shoot with blanks…

   When you give nothing but personal opinions it’s easy to confuse attacks on those with attacks on you.

   But it’s funny how if evolution is on it’s deathbed and supporters only have personal attacks in their armoury, how much worse must your theory be to be losing to one on it’s death bed?

10. Allan Miller

    And more is still being found and the list keeps growing.

    We have many similarities here but no discussion of differences and how they may have come about without Rumrakets puff process. The mitochondria not only generate ATP but are integrated into the cells control mechanisms. This is a very complex adaption and without the force play of “evolution is the only choice” I see good reason to be skeptical that this endyosyboitisc occurred.

11. colewd: This is a very complex adaption and without the force play of “evolution is the only choice” I see good reason to be skeptical that this endyosyboitisc occurred.

    What is the best explanation?

    The “choice” is dictated by the evidence. You have no explanation for the evidence, and the evolutionary explanation makes sense of it.

    If there is another meaningful explanation, then bring it. This isn’t your religion, you know, it’s a tentative “best fit.” Your “skepticism” serves no purpose other than to prop up your non-explanation. As best-fit at the time, the endosymbiosis hypothesis remains productive, your “skepticism” just says “no,” leading to the nothing that is your preference.

    Glen Davidson

12. I’m afraid Bill has no alternative explanation he’s willing to present. I think I know the one he’s unwilling to present, though. It’s interesting that he’s willing to accept very sketchy evidence for the resurrection of Jesus, but his standards change radically for any evolutionary hypothesis. One might speculate on the reasons for such flexible standards, but it might be against the rules.

13. colewd: endyosyboitisc occurred

14. colewd,

    We have many similarities here but no discussion of differences and how they may have come about

    You asked for evidence for the endosymbiosis theory. Now, you’re complaining that I didn’t do something else! What you meant to say was “thanks for going to the trouble of going to the internet and providing a comprehensive summary of the evidence for endosymbiosis, Al. You’re a good egg”.

    The mitochondria not only generate ATP but are integrated into the cells control mechanisms.

    Sure they are – now. Can’t you see any adaptive reason why progressive integration might have been beneficial? Does that preclude a less intimate association initially?

    This is a very complex adaption and without the force play of “evolution is the only choice” I see good reason to be skeptical that this endyosyboitisc [sci!] occurred.

    So what do you do with the evidence I presented? Sniff it suspiciously, then make sure your route home never passes that way again? I mean, why, on God’s green earth, would mitochondria and plastids and bacteria use N-formyl methionine as initiator? Because it’s all rilly rilly complex? The absence of intermediates during the lengthier run of eukaryogenesis is absolutely nothing to do with endosymbiosis itself. There is a list of facts above that your alternative theory needs to explain. Why is there extensive evidence of endosymbiosis, if endosymbiosis was too complicated to happen?

    You and J-Mac and Sal make the same mistake. You think that the endosymbiotic theory is intended to be a wrapper for the whole of eukaryogenesis. It isn’t.

15. dazz: I’m not arrogant enough to pretend that I understand this stuff all that well.

    LoL.

    You’re just arrogant enough to pretend that you understand this stuff well enough to tell other people that they are wrong and to mock them. You make a great poster boy for TSZ in general.

16. Allan Miller: You think that the endosymbiotic theory is intended to be a wrapper for the whole of eukaryogenesis.

    And he probably didn’t get that idea from evolutionists!

17. Mung,

    And he probably didn’t get that idea from evolutionists!

    No, he probably didn’t. I’m guessing you’re trying to suggest he did really, in your oblique way. But what I think is going on is half-grasped facts integrated with an aversion to accept anything an evolutionist actually says at face value. This point – endosymbiosis /= eukaryogenesis – has been made repeatedly in this thread, and no-one seems to want to take it on board. It’s not for want of trying.

18. Allan Miller: endyosyboitisc [sci![sic!]]

    Isn’t there a rule of the internet that every spelling flame must contain a spelling error?

19. John Harshman,

    It was deliberate, hence the exclamation mark. Honest!

20. Allan Miller: This point – endosymbiosis /= eukaryogenesis – has been made repeatedly in this thread, and no-one seems to want to take it on board. It’s not for want of trying.

    It’s bloody freaking obvious that endosymbiosis /= eukaryogenesis, the alternative being that endosymbiosis happened only once in the entire history of life making it indistinguishable from a miracle.

    Not that it would pose any problem for evolutionists if that were the case. Am I right?

21. Mung: happened only once in the entire history of life making it indistinguishable from a miracle.

    I miss Jesus’ days when miracles were dime a dozen

22. Mung,

    It’s bloody freaking obvious that endosymbiosis /= eukaryogenesis, the alternative being that endosymbiosis happened only once in the entire history of life making it indistinguishable from a miracle.

    No, that’s not the alternative. It’s just about separating out those eukaryote features that had nothing to do with endosymbiosis from those that did. Nor does happening once make something indistinguishable from a miracle. Anyways, happened twice (at least) in plants.

    Not that it would pose any problem for evolutionists if that were the case. Am I right?

    Not really an issue either way. Should it be?

23. It would cause an issue for evolution if everything that distinguishes eukaryotes from prokaryotes could be shown to have happened at once – cytoskeleton, telomeres, multiple origins of replication, spliceosomes, sex, organelles and other compartments, etc etc etc. But noting differences between deep-branching lineages is not the way to establish that this was indeed the case, since there is an obvious possibility for divergent lineages to become different piecemeal, with extinction of intermediate lineages, possibly by competition with the ‘enhanced’.

24. Is there a Universal Miraculousity Bound n?

    1 time = miracle!
    2 times = 2 miracles!!
    …
    n times, natural

25. I wouldn’t call it frequent, but intracellular endosymbiosis has happened a great many times. Every intracellular parasite is an example. And extracellular endosymbiosis has happened a lot too in multicellular organisms. Even if we restrict the cases to mutualism, it’s happened many times. There are cases of secondary endosymbiosis, in which some “algae” gained their plastids by engulfing other algae that harbored plastids. There is at least one case of tertiary endosymbiosis. There’s a species of sea slug that saves the plastids of the algae it eats and puts them to work. There are cases of incipient endosymbiosis, of bacterial species that are sometimes free-living and sometimes inside eukaryotic cells.

26. dazz: I miss Jesus’ days when miracles were dime a dozen

    I just love how your mind functions.

    If miracles were a dime a dozen then what do you suppose set Jesus apart from all the other miracle workers of his day?

    And then there’s the mocking that took place when he failed to perform a miracle. I can just see dazz standing there, mocking, along with the rest of the disbelievers.

    #PosterBoy

27. Allan Miller: Anyways, happened twice (at least) in plants.

    Therefore, it’s nothing unique to eukaryogenesis. So it’s bloody freaking obvious that endosymbiosis /= eukaryogenesis. Or should be.

28. Allan Miller: This point – endosymbiosis /= eukaryogenesis – has been made repeatedly in this thread, and no-one seems to want to take it on board. It’s not for want of trying.

    And given John’s nice post I have to wonder if anyone in this thread is actually arguing that endosymbiosis = eukaryogenesis. Because if they are, that would be bloody freaking ignorant. 🙂

29. Allan Miller: Why can’t God generate a space of possibilities that is connected by small steps, I wonder?

    No fair. Now you’re stealing my argument. You need to come up with your own arguments.

30. Mung,

    Therefore, it’s nothing unique to eukaryogenesis. So it’s bloody freaking obvious that endosymbiosis /= eukaryogenesis. Or should be.

    No, I sense a miscommunication. Endosymbiotic theory as an explanation of the origin of mitochondria/plastids is not the same thing as eukaryogenesis, is what I intended by my shorthand. I wasn’t suggesting that Bill et al thought that the totality-of-endosymbiosis was the proffered explanation for the distinctive features of eukaryotes. That would have been pretty silly, so I’d have hoped you might have realised that without me actually spelling it out.

    They seem to doubt endosymbiosis [as an explanation for the origin of mitochondria/plastids, I hope I am not going to have to type out every time I say it] because it does not explain the entirety of eukaryogenesis.

31. Mung,

    I should point out that the points made in ‘John’s nice post’ have also been made by me and RodW. But, see my prior post for why you have grabbed entirely the wrong end of the stick. And read the thread if you want to see how J-Mac, Sal and Bill have understood endosymbiosis [as it applies to the origin of mitochondria/plastids – can I stop now?] and its relation to eukaryogenesis.

32. Mung: what do you suppose set Jesus apart from all the other miracle workers of his day?

    I dunno… His beard?

33. Mung,

    No fair. Now you’re stealing my argument. You need to come up with your own arguments.

    So you think the space fully connected? That doesn’t chime with other things you’ve said, but that’s +1 for evolutionary theory at least.

34. Allan Miller: You and J-Mac and Sal make the same mistake. You think that the endosymbiotic theory is intended to be a wrapper for the whole of eukaryogenesis. It isn’t.

    I’ve reviewed all the comments of colewd in this thread and nowhere does he argue that endosymbiosis = eukaryogenesis.

35. Allan Miller: It was deliberate, hence the exclamation mark. Honest!

    I believe you. 🙂

    colewd: I see good reason to be skeptical that this endyosyboitisc occurred.

36. Allan Miller: So you think the space fully connected? That doesn’t chime with other things you’ve said, but that’s +1 for evolutionary theory at least.

    I don’t have an opinion yet about whether the space is fully connected. But if it is fully connected, I can find an argument for ID in that.

    My version of ID is very flexible. 🙂

37. dazz: I dunno…

    Truer words…

38. Endyosyboitisc is the cdesign proponensists alternative to endosymbiosis, right?

39. Mung,

    I’ve reviewed all the comments of colewd in this thread and nowhere does he argue that endosymbiosis = eukaryogenesis.

    He appears to regard endosymbiosis as evolutionists’ ‘best guess’ on the complexities of eukaryogenesis. If that is not what he actually thinks, I would be more than happy to withdraw.

    What of Sal and J-Mac? I mean, there is a whole freaking OP up above. Is he not conflating the two?

40. Mung: I just love how your mind functions

    By the way…

    Mung: If miracles were a dime a dozen

    I love how your mind functions, you somehow think I believe, conceded or even contemplated the possibility that Jesus performed miracles. How cute

41. Allan Miller: What of Sal and J-Mac? I mean, there is a whole freaking OP up above. Is he not conflating the two?

    According to John the OP is incoherent. So I think maybe I’ll start with Sal’s posts next. Because, you know, his posts are never incoherent.

42. dazz:
    Endyosyboitisc is the cdesign proponensists alternative to endosymbiosis, right?

    I believe it’s the source of covfefe.

43. This is one of the most fundamental mysteries of evolution and the origins of multicellular life often called endosymbiosis, which is supposed to explain the origin of eukaryotic cell.

    I have to wonder why the first words out of anyone here in this thread didn’t point out the obvious difference between the origin of multicellular life and the origin of the eukaryotic cell.

44. It never ceases to amaze me how some people absolutely revel in being ignorant. It’s like the Gospel for them. Ignorance becomes a virtue. We’re ignorant! We’re ignorant! Therefore ID is false!

    ok, sure, whatever …

45. Mung,

    I have to wonder why the first words out of anyone here in this thread didn’t point out the obvious difference between the origin of multicellular life and the origin of the eukaryotic cell.

    A correction available to both evolutionist and Creationist alike, of course.

46. Allan Miller: A correction available to both evolutionist and Creationist alike, of course.

    Of course. I think you’ll find that’s my first comment on the actual content of the OP. Am I really the first person to bring it up?

47. Mung,

    Am I really the first person to bring it up?

    Yep – ‘good catch’, I believe is the appropriate term.

    J-Mac, indeed TSZ as a whole, is competing for my attention with various tabs whose nature I am not at liberty to disclose, is my excuse …

48. Allan Miller: J-Mac, indeed TSZ as a whole, is competing for my attention with various tabs whose nature I am not at liberty to disclose, is my excuse …

    ok, well, I just googled “popped a tab” and I can see why you wouldn’t be interested in full disclosure.

49. Mung: I have to wonder why the first words out of anyone here in this thread didn’t point out the obvious difference between the origin of multicellular life and the origin of the eukaryotic cell.

    In total honesty, I saw J-mac wrote the post and so didn’t even bother reading all the way through it. My immediate reflex upon seeing him as the author is the same as when I see a post by Rober Byers: Don’t bother.

50. Mung,

    Allan Miller August 26, 2017 at 9:39 pm
    Mung,

    Therefore, it’s nothing unique to eukaryogenesis. So it’s bloody freaking obvious that endosymbiosis /= eukaryogenesis. Or should be.

    No, I sense a miscommunication. Endosymbiotic theory as an explanation of the origin of mitochondria/plastids is not the same thing as eukaryogenesis, is what I intended by my shorthand. I wasn’t suggesting that Bill et al thought that the totality-of-endosymbiosis was the proffered explanation for the distinctive features of eukaryotes. That would have been pretty silly, so I’d have hoped you might have realised that without me actually spelling it out.

    They seem to doubt endosymbiosis [as an explanation for the origin of mitochondria/plastids, I hope I am not going to have to type out every time I say it] because it does not explain the entirety of eukaryogenesis.

    Can you guys send a note to my alma mater UC Berkeley. They did not get the memo that endosymbiosis /= eukaryogenesis.

    From their evolution website:

    When you look at it this way, mitochondria really resemble tiny bacteria making their livings inside eukaryotic cells! Based on decades of accumulated evidence, the scientific community supports Margulis’s ideas: endosymbiosis is the best explanation for the evolution of the eukaryotic cell.