A Prediction Tested

Several themes have been doing the rounds lately. The origin of organelles, standards of evidence, common descent, the role of phylogenetic analysis, and the meaning of ‘prediction’ in science. Here’s a case study/rambling discourse that links a few themes.

Researching an answer to a separate question (I do try), I was struck by a thought about RecA. RecA (also going by the names RAD51, Dmc1 and RADA in different groups, for historical reasons) is a ubiquitous group of proteins involved in homologous DNA repair. That’s a process whereby a break in DNA can be ‘patched’ if a homologous sequence can be located. Matching sequence either side of the gap is aligned (by nothing more sophisticated than the binding energy of DNA complementarity) and then a DNA polymerase template-copies from the intact strand to the broken one between the two complementary sequences. Both accidental and deliberate breaks are repaired by this, hence it is involved both in maintaining DNA integrity and in the more ‘orchestrated’ process of crossover formation in meiosis.

Because this process relies on quite a high degree of complementarity, it works best on sister chromosomes – those recently replicated, within the current cell cycle, and hence clearly commonly descended. This is all a prokaryote has to work with, outside of instances of LGT. In eukaryotic diploids, the donor for repair can be the homologous diploid chromosome (that’s a terminological confusion: the chromosome pair with the greatest amount of homology is actually not the homologous pair, but the sister pair). But even in diploids, the sister is ‘preferred’ for repair – when not available, the normal repair pathway is ‘nonhomologous end joining’, which simply splices the break. An exception to this is during crossover of meiosis. Most crossovers form between homologues, not sisters.

So, thinks I, if chloroplasts and mitochondria evolved from bacteria, their RecA equivalents should be more like those of bacteria than archaea. To the internet!

It so happens that all these proteins are, in the modern eukaryote, held in nuclear DNA. So in a plant, you’ve got your RAD51s, plus Dmc1 specific to meiosis, but you’ve also got RecA proteins targeting, respectively, mitochondria and chloroplasts. RECA1 heads for chloroplasts, RECA3 for mitochondria. There’s also RECA2 which goes to both.

More specific and comprehensive phylogenetic analysis reveals quite a complex picture. Nonetheless, the Lin paper notes a ‘striking’ sequence similarity between the recA genes of plants and protists and those of the bacteria from which they are presumed to have come. There is a healthy 61% sequence match between RECA1 and the RecA of cyanobacteria. Sequence identity for RECA3/bacteria is not so high, but interestingly, Arabidopsis RECA3 can complement E. coli deficient in bacterial recA. E. coli are Gammaproteobacteria, not Alphaproteobacteria as is thought to be the group from which mitochondria came, but still not a million miles away. That’s not conclusive of a common origin, but is a noteworthy fact, consistent with structural conservation.

And that, really, is where I was headed. I started from the hypothesis that mitochondria and chloroplasts originated as bacteria. A prediction of that hypothesis is that organelle-targeted proteins would be expected in general to align more closely with bacterial than with archaeal or non-organellar eukaryote proteins. That prediction has been borne out. The hypothesis has been strengthened by that observation. How can that be? I did the same a few days ago with N-formyl methionine as translation initiator. Maybe I’m cherry-picking, but there are no searches I’m not mentioning that drew a blank. This is the sum total of my ‘research’: two things that it occurred to me to look for, and I found them both.

Also of interest to me, given the conviction explored in my ‘Evolution of Sex’ paper that meiosis is foundational to the modern eukaryote clade, is the finding that Dmc1 apparently evolved very early during what it pleases me to call ‘eukaryogenesis’. Whether it preceded or succeeded the mitochondrial endosymbiosis is not clear, which is one reason I don’t think of endosymbiosis as definitively the origin of the eukaryotic cell, whatever lols may accompany someone finding an author who does just that (Hi, Mung!).

Another point to ponder: homologous recombination relies upon a physical analogue of the algorithmic alignment performed during sequence comparison. It is only by anchoring matching sequences that ‘differences’ – in repair, the missing vs the intact sequence – can be located. Molecular differences between taxa are trumpeted by Creationists, but they are located in much the same way. The question remains: where does the alignment come from? In the case of sister chromosomes, it is non-controversially common descent – the sisters arise in the same cell cycle. In the case of diploid homologues, again not too controversial – the bases of the haploid chromosomes in gametes can reasonably be assumed to have a common origin in template-copies originating in an ancestral cell. But somehow, for the Creationist, this logic breaks down somewhere not clearly specified outside of the species. Alignment suddenly stops being common descent and becomes the completely indistinguishable ‘common design’. I don’t see why.

206 thoughts on “A Prediction Tested

  1. phoodoo,

    Right, so I just showed you a quote from Darwin, where he claimed it would be slow steps

    Also gradual steps. But to the extent that someone thought evolution is limited in speed (how are you measuring that? Darwin certainly doesn’t say), I guess one might say that prediction has not been borne out, if someone had put an actual limit on it that has been transgressed. But no such limit was placed. You have interpreted Darwin specifically to exclude the lizards, somewhat arbitrarily.

    Endosymbiosis would be better for the case you are trying to make. It is clear that endosymbiosis is not ‘gradual’ in the sense Darwin meant. So, it falsifies strict gradualism. That does not make endosymbiosis a prediction of evolutionary theory – quite the contrary. So why are you saying people claim it is?

  2. Allan Miller: Also gradual steps. But to the extent that someone thought evolution is limited in speed (how are you measuring that? Darwin certainly doesn’t say), I guess one might say that prediction has not been borne out, if someone had put an actual limit on it that has been transgressed. But no such limit was placed. You have interpreted Darwin specifically to exclude the lizards, somewhat arbitrarily.

    Exclude the lizards, what?? How have i interrupted Darwin to exclude the lizards, that makes no sense at all.

    Listen I greatly appreciate the lengths you are willing to go to demonstrate so clearly how the Lucky Accidenters revise history to include any new findings. Your latest revision is that no speed limits were ever placed, so it fits the theory just fine.

    Thank you for your generosity in making my point Allan.

  3. phoodoo,

    Exclude the lizards, what?? How have i interrupted Darwin to exclude the lizards, that makes no sense at all.

    Since no actual figure has been placed on evolutionary rate, we can’t be sure how to interpret ‘slow’, Did Darwin definitively mean ‘greater than 36 years’? And how much actual change was he talking about? How did these never-mentioned figures get plugged into evolutionary theory? How has the lizard data affected evolutionary theory since?

    What about mosquitoes Plasmodium? They evolved chloroquine resistance much more quickly than 36 years. Antibiotic resistance? I don’t see anyone going back to evolutionary theory and adjusting a nonexistent ‘rate’ parameter in light of these examples.

    Anyway, back to endosymbiosis. Where is the prediction that endosymbiosis would occur?

  4. Allan Miller: Endosymbiosis would be better for the case you are trying to make. It is clear that endosymbiosis is not ‘gradual’ in the sense Darwin meant. So, it falsifies strict gradualism.

    🙂

  5. Allan Miller,

    Allan, its pretty simple really. if these examples were not predicted by Darwinian evolution, then they either or contrary to the theories predictions, or you are simply being a revisionist, and saying, “Oh, we never made any predictions about that actually, so its no problem for the theory of evolution. Its just what we should expect”

    So when you claimed it was the creationists doing revisionist history, instead you have just shown your lack of awareness of the Lucky Accidenters revisionism. You can keep trying to clutch a branch on the way down, but I have already shown you.

    Will you acknowledge it? Of course not. You are a Lucky Accidenter, they never acknowledge their defeats. It makes it so much easier to claim how robust their theory is.

  6. phoodoo: Allan, its pretty simple really. if these examples were not predicted by Darwinian evolution, then they either or contrary to the theories predictions, or you are simply being a revisionist, and saying, “Oh, we never made any predictions about that actually, so its no problem for the theory of evolution. Its just what we should expect”

    This is just not correct. A theory can be compatible with a set of observations, without explicitly predicting them.

    To pick an example from another scientific field, the theory of plate tectonics does not predict that there will some times be very large craters in the surface of our planet, despite actually being a theory about the kinds of structures we should expect to see make up the surface of our planet.

    Nevertheless, craters exist but were not predicted by the theory of plate tectonics, yet the theory is entirely compatible with the existence of craters. Finding craters does not falsify plate tectonics.

  7. phoodoo,

    Allan, its pretty simple really. if these examples were not predicted by Darwinian evolution, then they either or contrary to the theories predictions, or you are simply being a revisionist, and saying, “Oh, we never made any predictions about that actually, so its no problem for the theory of evolution. Its just what we should expect”

    How in hell can it be ‘revisionist’ to say that a particular prediction has not been made if a particular prediction has not, in fact, been made? So no, of course I won’t ‘acknowledge it’.

    Here’s the Phoodoo Version: evolutionists say their theory predicted something, even if it didn’t. Supporting evidence? Interpretation of the word ‘slow’ in a 160-year-old book.

    Of course, theories can be revised, and it would be strange to be critical of a theory simply because it is not unchangeable dogma. But your contention does not hold water on endosymbiosis – the ToE has not been revised to accommodate it, and no-one has ever said ‘that’s what we expect’. To support your original contention, you have to find someone saying, before during or after, “endosymbiosis is predicted by the theory of evolution”. I predict you will find no such evidence. Which is strange, because you had hundreds of examples lined up, you told me.

  8. Allan Miller: But your contention does not hold water on endosymbiosis – the ToE has not been revised to accommodate it…

    Why on earth would you write such a thing? Sure it has.

    And let’s not forget that the idea was initially rejected by evolutionists, and one would at least hope that they had some reason for doing so.

  9. Allan Miller,

    I not only provided you with an example, I even gave a quote from Darwin. And you did what all Lucky Accidenters do when they want to wriggle out of something. You said, “Oh, well, Darwin didn’t say what SLOW meant! Oh Darwin wasn’t talking about lizards. Oh, He just said slow, he didn’t put a limit on how slow….yadda yadda. ”

    Textbook revisionism Allan, just as I predicted! Why would I need to use your example, when I already gave you one and you proved me right so easily.

    Lucky Accidenters are so predictable.

  10. phoodoo,

    “Oh, well, Darwin didn’t say what SLOW meant! Oh Darwin wasn’t talking about lizards. Oh, He just said slow, he didn’t put a limit on how slow….yadda yadda. ”

    So how exactly has your contention been supported by all this verbiage? If Darwin did not specify a limit, how are we to suppose there has been ‘revision’ in light of the lizards?

  11. phoodoo: Lucky Accidenters are so predictable.

    Well, at least he changed his mind about gradualism. Which isn’t to say that he won’t change it right back again. 🙂

  12. Mung,

    Why on earth would you write such a thing? Sure it has.

    All endosymbiosis is, as far as the ToE is concerned, is another source of variation – an instance of gene transfer.

  13. Mung,

    Well, at least he changed his mind about gradualism. Which isn’t to say that he won’t change it right back again

    Prove it. Prove that I ever said endosymbiosis was ‘gradual’. This is skating very close to lying.

  14. Allan Miller: Prove it. Prove that I ever said endosymbiosis was ‘gradual’. This is skating very close to lying.

    Chill Allan. Why should I have to prove a claim I didn’t make?

    I didn’t say that you said that endosymbiosis was ‘gradual’. [Though you rather obviously DO believe that.] For example, do you actually believe that the transfer of the genes from the bacterial DNA to the nuclear DNA happened all at once?

    By the way, there’s another hypothesis for you to test should you care to do so. Where, in the nuclear DNA, are these genes located relative to each other?

  15. Mung,

    I didn’t say that you said that endosymbiosis was ‘gradual’. [Though you rather obviously DO believe that.]

    To be honest, the jury’s out. I am prepared to grant arguendo that endosymbiosis may be an exception to strict Darwinian ‘gradualism’. Sex too, come to that, and whole-genome or whole-chromosome duplication, allopolyploidy and so on. So what I ‘obviously believe’ may not accord with what I actually do believe.

    For example, do you actually believe that the transfer of the genes from the bacterial DNA to the nuclear DNA happened all at once?

    No. But then that’s not quite endosymbiosis per se but something that came after (or before – see below). What I am prepared to grant as a possibility is that a very rapid event (measured in hours) may have led to the formation of a new kind of organism, which has since been subject to much evolutionary tinkering. It’s the encapsulation of two genomes in one cell that is significant – the moment their fates become linked – rather than some point their genomes have undergone an undefined amount of merger. But equally, I can conceive of ‘gradual endosymbiosis’ – such as the Ignicoccus/Nanoarchaeon system I have mentioned as a possible model. One can regard as a ‘big bang’ the moment the smaller cell became engulfed in the larger cell’s cytoplasm, but gene transfer may conceivably have preceded this.

    I have no strong loyalty to gradualism itself. I don’t see what is gained or lost by insisting having change be below a threshold. Enormous leaps are obviously less likely, but it is not dichotomous or subject to a hard boundary. Really, the chap you want to speak to about that is Charles Darwin. You’ll find him in Westminster Abbey. You might need to bring him up to speed on some things – genetics, for example.

    By the way, there’s another hypothesis for you to test should you care to do so. Where, in the nuclear DNA, are these genes located relative to each other?

    What’s the hypothesis?

  16. Allan Miller: What’s the hypothesis?

    That they were [or were not] copied into the nuclear DNA piecemeal. Take your pick. 🙂

    Would you consider it more surprising if they were in a contiguous region or if they were dispersed?

    If we look at bacteria alone, how are their genes for their DNA repair proteins distributed in the bacterial genomes?

    In the eukaryotes, how are the genes for mitochondrial DNA [ETA: or chloroplast DNA] repair distributed relative to the genes for nuclear DNA repair?

    There’s no ‘gotcha’ lurking here. I’m just inquisitive. Like I said, I truly enjoyed your OP. not only for the questions it raised and answered but also for the additional questions that it brings to mind. Makes me think. 🙂

  17. Allan Miller: To be honest

    I really appreciate it when people begin their sentence with To be honest
    For some reason, it makes me feel assured that the had not been bulls…ting before… 😉

  18. Mung,

    That they were [or were not] copied into the nuclear DNA piecemeal. Take your pick.

    I’m not sure that information is directly available. There have been about 1.5 billion years of evolution since the event, if you believe those morons who aren’t convinced of 6000 years by a few lumps of coal. Genes appear to be quite mobile, on that sort of scale. I would expect, simply from cell physiology, that uptake into the nucleus from the cytoplasm is restricted by the size of molecule that can get through nuclear pores, which argues for smaller fragments. The arguments I sketched in two posts above would also tend to apply to just one or two genes at a time.

    On the other hand, since nuclear DNA is already in the nucleus (duh!), wholesale shuffling is likely to erode any signal that there was of gene order if larger fragments formed the initial transfer.

  19. Allan Miller: I would expect, simply from cell physiology, that uptake into the nucleus from the cytoplasm is restricted by the size of molecule that can get through nuclear pores, which argues for smaller fragments.

    You believe the host archeon had a nucleus already, replete with nuclear membrane? Because I’ve been telling Rumraket that there is no evidence for that hypothesis. Do any extant archea have a nucleus?

  20. Allan Miller: Genes appear to be quite mobile, on that sort of scale.

    On what sort of scale are genes not mobile, lol? For a minute there I thought you were denying that sequences close together in the DNA could be used to infer degree of relatedness. Whew!

  21. Mung,

    You believe the host archeon had a nucleus already, replete with nuclear membrane?

    I have no idea as far as the mitochondrion is concerned. The sequence of events in eukaryogenesis is behind the ‘event horizon’ of LECA. For the chloroplast, then yes, there was a nucleus.

    Nonetheless, if there was a nucleus at some stage during the mitochondrial transfer, it would restrict the size of molecules allowed to pass from that point on. The older you go, the more scrambled the nuclear genome; the more recent you go, the more likely biased to small size by nuclear pores. So either way, I would not expect to detect a signal from larger transfers.

  22. Hang on Allan, aren’t all religions popular?

    ETA: Excepting your own religion, Allanism. It’s the odd one out.

    ETA: ETA: You need to describe the rewards, not just the punishments. Virgins. Phylogentic trees bearing all sorts of fruits. Sudden appearances.

  23. Allan Miller: I would expect, simply from cell physiology, that uptake into the nucleus from the cytoplasm is restricted by the size of molecule that can get through nuclear pores, which argues for smaller fragments.

    This in turn presumes the nucleus existed before the initial engulfing of the mitochondrial ancestor, which is subject to much debate. I’m not aware (though that is not itself meant as an argument) of any data that couldn’t be rationalized either way.

    To my knowledge some of the genes of the nuclear pore complex are homologous to bacterial membrane transporters of some sorts. Not to mention the fact that the plasma and nuclear membrane is made up of the same ester glycerol lipids found in bacteria (and the enzymes that biosynthesize them are homologous).

    Some have suggested that this implies the nucleus evolved after the acquisition of proto-mitochondrial genes and that a contributing factor to the development of the nucleus was in part as an adaptation to avoid interference from the genomes of lysing mitochondria.

  24. Rumraket,

    True, though the argument applies with more force to chloroplasts.

    Membranes as a whole appear to have come from the bacterium, but this does not necessarily mean that the whole genome moved before the nucleus was encapsulated.

  25. Allan Miller: Nope, just me so far.

    Do you worship yourself? And if I join your religion, would I worship you or would I worship myself, or would I worship something like a spaghetti strainer?

  26. Mung: Do you worship yourself? And if I join your religion, would I worship you or would I worship myself, or would I worship something like a spaghetti strainer?

    You worship the spaghetti not the strainer, wearing the strainer is a sign of respect

  27. Mung,

    Do you worship yourself?

    Nah – what kind of an egotistical bastard do you think I am? I get everyone else to worship me.

  28. Mung: Allanism makes sense to me. Does that make me a believer?

    Not necessarily, j-Mac said it has to make sense, not that it does make sense

  29. Can the desire for parsimony go too far?

    In this chapter we put forth a more parsimonious hypothesis, namely that both mitochondria and chloroplasts originated through the single endosymbiont event of a host cell engulfing a cyanobacterium. We propose that a cyanobacterium could have been engulfed by a proto-eukaryote in an extremely unlikely rare-chance event very early in evolution.

    – An Alternative Hypothesis for the Origin of Mitochondria

    So. Sort of like a miracle. An “evolutionary singularity.” The history of life must be replete with such events. Are miracles detectable after all?

  30. Couple of things:

    First, different major taxa have different numbers and identities of genes transferred from mitochondria to the nucleus, which suggests that it’s a gradual thing. Similarly, copying of mitochondrial genes to the nucleus is still going on, though without subsequent loss, so far. Many species of birds have large, contiguous fractions of the mitochondrial genome present as copies in the nucleus. Such sequences are called numts, which you could google if you liked. And again, this suggests that transfer is not difficult, even when there’s a nuclear membrane.

  31. The current view of of an a-proteobacterial origin of mitochondria rests on the remarkable similarity of the amino acid sequences of mitochondrial proteins to corresponding a-proteobacterial proteins. We argue that phylogenetic evidence based solely on aminoacid sequence similarity must be treated with caution.

    – An Alternative Hypothesis for the Origin of Mitochondria

    Is “must be treated with caution” like saying “must be taken with a grain of salt”?

  32. Mung,

    Is “must be treated with caution” like saying “must be taken with a grain of salt”?

    So maybe it was a gammaproteobacterium? That it was a bacterium of some kind is supported by evidence outside of sequence alignments. Such as N-formyl methionine. I think you might be over-interpreting the note of caution.

  33. Mung: Is “must be treated with caution” like saying “must be taken with a grain of salt”?

    It is entirely possible that a different clade of bacteria will in time turn out to be a better match for the ancestor of mitochondria and chloroplasts. I have a hard time imagining that the particular species of bacterium really “matters” to anyone. The take home message seems to be that there can be some ambiguity about the exact nature of the symbiont, but this is a far cry from saying we can’t have very convincing reasons that endosymbiosis took place.

  34. Allan Miller:
    phoodoo: How did life arise? “Well, it just did, why do you have to know everything?”

    Allan: We got to the origin of life in 5. Is this a record? Probably not.

    Now if I could only find a name for my new law.

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