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

1. Congratulations on your OP. I loved the illustrations.

   With regard to the origin of eukaryotes, this page looks interesting:

   Origin of Eukaryotes (Lipscomb Lab Web Site). It is critical of endosymbiosis and puts forward other hypotheses.

   For a pro-endosymbiosis view, see Endosymbiosis and The Origin of Eukaryotes (Kimball’s Biology Pages, an online biology textbook by John W. Kimball, who taught at Harvard.)

   I also came across this 2015 article by Dr. Eugene Koonin, who defends a version of emdosymbiosis:

   Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier? (Philosophical Transactions of the Royal Society of London B, Biological Sciences 2015 Sep 26; 370(1678): 20140333. doi: 10.1098/rstb.2014.0333.) From the abstract:

   The origin of eukaryotes is a fundamental, forbidding evolutionary puzzle. Comparative genomic analysis clearly shows that the last eukaryotic common ancestor (LECA) possessed most of the signature complex features of modern eukaryotic cells, in particular the mitochondria, the endomembrane system including the nucleus, an advanced cytoskeleton and the ubiquitin network. Numerous duplications of ancestral genes, e.g. DNA polymerases, RNA polymerases and proteasome subunits, also can be traced back to the LECA. Thus, the LECA was not a primitive organism and its emergence must have resulted from extensive evolution towards cellular complexity. However, the scenario of eukaryogenesis, and in particular the relationship between endosymbiosis and the origin of eukaryotes, is far from being clear. Four recent developments provide new clues to the likely routes of eukaryogenesis. First, evolutionary reconstructions suggest complex ancestors for most of the major groups of archaea, with the subsequent evolution dominated by gene loss. Second, homologues of signature eukaryotic proteins, such as actin and tubulin that form the core of the cytoskeleton or the ubiquitin system, have been detected in diverse archaea. The discovery of this ‘dispersed eukaryome’ implies that the archaeal ancestor of eukaryotes was a complex cell that might have been capable of a primitive form of phagocytosis and thus conducive to endosymbiont capture. Third, phylogenomic analyses converge on the origin of most eukaryotic genes of archaeal descent from within the archaeal evolutionary tree, specifically, the TACK superphylum. Fourth, evidence has been presented that the origin of the major archaeal phyla involved massive acquisition of bacterial genes. Taken together, these findings make the symbiogenetic scenario for the origin of eukaryotes considerably more plausible and the origin of the organizational complexity of eukaryotic cells more readily explainable than they appeared until recently….

   A major problem faced by this scenario (and symbiogenetic scenarios in general) is the mechanistic difficulty of the engulfment of one prokaryotic cell by another [20,28,29,38]. Although bacterial endosymbionts of certain proteobacteria have been described [39,40], such a relationship appears to be a rarity. By contrast, in many unicellular eukaryotes, such as amoeba, engulfment of bacterial cells is routine due to the phagotrophic lifestyle of these organisms [20]. The apparent absence of phagocytosis in archaea and bacteria prompted the reasoning that the host of the proto-mitochondrial endosymbiont was a primitive phagotrophic eukaryote, which implies the presence of an advanced endomembrane system and cytoskeleton [20,28,29,38]. Thus, argument from cell biology seemed to justify rescuing the archezoan scenario, the lack of positive evidence notwithstanding.

   However, comparative analysis of the increasingly diverse collection of archaeal and bacterial genomes has yielded multiple lines of evidence that might change the notion of the implausibility of an archaeo-bacterial endosymbiosis. In this article, I discuss the results of genome evolution reconstructions that imply complex ancestral archaeal forma and the discovery of the dispersed archaeal ‘eukaryome’. The eukaryome consists of multiple genes identified in different archaea that encode key components of the cytoskeleton, the cell division apparatus, the ubiquitin system and other signature eukaryotic cellular systems. A complementary line of recent developments shows that massive acquisition of bacterial genes probably occurred on multiple occasions in the course of the evolution of archaea. Taken together, these findings seem to be making the scenario of archaeo-bacterial symbiosis considerably more plausible than it appeared even recently…

   Acquisitions of numerous bacterial genes that amount to genomic chimaerism and lead to substantial remolding of cell physiology and emergence of groups with new lifestyles appears to be a recurrent rather than unique event in evolution, at least in archaea. Could it be that most if not all major groups of archaea emerged from botched endosymbiotic events? Should that be the case, eukaryogenesis only differs in that the endosymbiont survived, retaining part of its physical and genetic identity…

   Arguably, the greatest difficulty faced by the endosymbiotic scenarios of eukaryogenesis is the apparent implausibility (or at least extreme rarity) of the engulfment of one prokaryotic cell by another. The recent advances of comparative genomics, complemented by the progress in the cell biology of archaea, seem to be closing this gap. Combined with the quantitative findings of genome evolution reconstructions on extensive differential gene loss in most archaeal lineages, the discovery of the ‘dispersed’ archaeal eukaryome implies a highly complex archaeal ancestor of eukaryotes [78,86]. Conceivably, this ancestral form possessed advanced cellular organization and certain ‘eukaryote-like’ functional capacities provided by the ancestral versions of various eukaryotic functional systems that are represented in different lineages of extant archaea (figure 1). The critical point is that the hypothetical eukaryotic ancestor probably possessed a cytoskeleton that consisted of both actin filaments and tubulin microtubules and could provide for a primitive phagocytic capacity [82,110]…

   Finally, the indications that massive acquisition of bacterial genes most probably triggered the emergence of the major groups of archaea put the origin of eukaryotes into a more general evolutionary context. These discoveries make the origin of eukaryotes appear less dramatically different from the origin of other groups of organisms than is generally perceived. Horizontal transfer of numerous genes appeared to have been central in each case. The key difference is that in eukaryotes the source of the foreign genes, i.e. the endosymbiont, survived as an organelle, precipitating the radical restructuring of the cell. Given the likely origin of eukaryotes from within the archaeal diversity and the observations on the dispersed eukaryome, there seems to be high promise of new evolutionary insights coming from metagenomics and single-cell genomics. The discovery of archaeal descendants of the elusive host of the mitochondrial endosymbiont cannot be ruled out.

   Addendum:

   Shortly after this manuscript was submitted, a game-changing discovery bearing on the archaeal ancestry of eukaryotes has been published [161,162]. Deep metagenomic sequencing uncovered a remarkable group of archaea from marine sludge that combined the two key properties expected of the eukaryotic ancestor. First, one of these novel organisms, tentatively classified as a new phylum Lokiarchaeota (already affectionately known as Loki), represents a sister group to eukaryotes, and the Loki–eukaryote branch is confidently lodged deep within the TACK superphylum. Second, the genome of Loki recapitulates with an uncanny precision the reconstructed gene repertoire of the putative archaeal ancestor of eukaryotes that is outlined above.

   Thoughts?

   Finally, here’s a recent article from Science Daily (On the origin of eukaryotes: When cells got complex, February 3, 2016):

   In a study published in the journal Nature, Centre for Genomic Regulation researchers Toni Gabaldón and Alexandros Pittis are shedding light on one of the most crucial milestones in the evolution of life: cells’ acquisition of mitochondria…

   “Like archeologists, we are trying to reconstruct something that existed in the past based on the evidence we have today. Specifically, we’ve tracked down proteins common to all complex organisms, and reconstructed their evolution. We found that the proteins related with mitochondria acquisition arrived later than those related with other parts of the cell,” states the study’s principal investigator, Toni Gabaldón. The scientists used a diverse set of measurements to date the incorporation of several proteins into the eukaryotic lineage. They found that the arrival of proteins had come in a number of “waves,” and that those related with ancestral mitochondria matched those of the latest wave. “Our work demonstrates that the acquisition of mitochondria occurred late in cell evolution, and that the host cell already had a certain degree of complexity,” states Alexandros Pittis, lead author of the study.

   Here’s the paper in Nature:

   The origin of eukaryotes stands as a major conundrum in biology[1]. Current evidence indicates that the last eukaryotic common ancestor already possessed many eukaryotic hallmarks, including a complex subcellular organization[1, 2, 3]. In addition, the lack of evolutionary intermediates challenges the elucidation of the relative order of emergence of eukaryotic traits. Mitochondria are ubiquitous organelles derived from an alphaproteobacterial endosymbiont[4]. Different hypotheses disagree on whether mitochondria were acquired early or late during eukaryogenesis[5]. Similarly, the nature and complexity of the receiving host are debated, with models ranging from a simple prokaryotic host to an already complex proto-eukaryote[1, 3, 6, 7]. Most competing scenarios can be roughly grouped into either mito-early, which consider the driving force of eukaryogenesis to be mitochondrial endosymbiosis into a simple host, or mito-late, which postulate that a significant complexity predated mitochondrial endosymbiosis[3]. Here we provide evidence for late mitochondrial endosymbiosis. We use phylogenomics to directly test whether proto-mitochondrial proteins were acquired earlier or later than other proteins of the last eukaryotic common ancestor. We find that last eukaryotic common ancestor protein families of alphaproteobacterial ancestry and of mitochondrial localization show the shortest phylogenetic distances to their closest prokaryotic relatives, compared with proteins of different prokaryotic origin or cellular localization. Altogether, our results shed new light on a long-standing question and provide compelling support for the late acquisition of mitochondria into a host that already had a proteome of chimaeric phylogenetic origin. We argue that mitochondrial endosymbiosis was one of the ultimate steps in eukaryogenesis and that it provided the definitive selective advantage to mitochondria-bearing eukaryotes over less complex forms.

   These are recent papers that I’m quoting from. Doolittle’s Uprooting the Tree of Life is powerfully argued, but dates back to the year 2000.

2. Excellent OP.

   Endosymbiosis doesn’t explain chromatin evolution.

   One aspect of chromatin evolution is the evolution of double-strand break repair mechanism unique to eukaryotes.

   The complexity of this boggles the mind, and like so many things about Eukaryotes, this system looks it was poofed into existence without an ancestor.

   I talked to a Theistic Darwinist when I was at Lipscomb University this last June, and even he admitted chromatin (unique to Eukaryotes) suggested a miracle.

   http://www.nature.com/nrm/journal/v15/n1/full/nrm3719.html

3. Thanks vjtorley!

   It’s always a great pleasure to read your thorough OPs and comments…I’ve always admired that about you…
   I, however, have neither the patience to write or to read long papers, OPs or comments…It’s just me…I guess… 😉

   When I write or even think about an OP or a comment, I always keep in mind the average readers…perhaps some who never comment or have a limited knowledge on the theme…

   Let’s face it; even an overwhelming amount of evidence is not going to change the mind of those who do want to change their views…just like I wrote at the conclusion of this OP…

   So, I my goal is to reach those who are searching for the truth and help them from what I want to convey…I believe the key to it is simplicity and few main points, or perhaps only one, but clearly and concisely developed…

   I know an amazing public speaker…I’m in awe each time when I listen to him speaking even on boring subjects… Why? Because he has a gift of making a boring theme an interesting one…How? What I wrote above are pretty much his keys to success though he does claim that public speaking is harder than writing…

   “These are recent papers that I’m quoting from. Doolittle’s Uprooting the Tree of Life is powerfully argued, but dates back to the year 2000.

   I’m well aware that this article is old…However that’s the only article on the theme of endosymbiosis that contained the specific statement I was looking for; regarding the missing genes…

   The missing genes have not been found have they??? 😉

4. stcordova:
   Excellent OP.

   Endosymbiosis doesn’t explain chromatin evolution.

   One aspect of chromatin evolution is the evolution of double-strand break repair mechanism unique to eukaryotes.

   The complexity of this boggles the mind, and like so many things about Eukaryotes, this system looks it was poofed into existence without an ancestor.

   I talked to a Theistic Darwinist when I was at Lipscomb University this last June, and even he admitted chromatin (unique to Eukaryotes) suggested a miracle.

   http://www.nature.com/nrm/journal/v15/n1/full/nrm3719.html

   Wow! I was thinking of you and the talk you gave on chromatin a while back…

   Awesome! Thanks Sal! 🙂

   BTW: I have been researching quantum physics such as quantum mechanics and the poofed into existence miracle or creation doesn’t look so magical on the subatomic level…the creation could be and probably will be explained on that level which is pretty new but growing…fascinating stuff man 🙂

5. LOL! gotta love ID-Creationist “logic”. Science can’t explain every last detail of events which happened a billion years ago. Therefore that makes the other 9,999,999 things science can explain about evolution be all wrong.

   And they still wonder why they are referred to as IDiots.

6. Adapa:
   LOL!gotta love ID-Creationist “logic”.Science can’t explain every last detail of events which happened a billion years ago. Therefore that makes the other 9,999,999 things science can explain about evolution be all wrong.

   And they still wonder why they are referred to as IDiots.

   And ID explains nothing about anything.

   Yet somehow in their minds that’s no strike against such a pathetically useless idea.

   Glen Davidson

7. Adapa:
   LOL!gotta love ID-Creationist “logic”.Science can’t explain every last detail of events which happened a billion years ago. Therefore that makes the other 9,999,999 things science can explain about evolution be all wrong.

   And they still wonder why they are referred to as IDiots.

   Make that 9.999.998…You forgot about the origins of life…

8. Adapa,

   Make that 9.999.997…You forgot about the origins of information…

9. J-Mac: Make that 9.999.998…You forgot about the origins of life…

   So the score is

   Science = 9, 999,998
   Unknown = 2
   ID-Creationism = 0

   Looks like the IDiots are still sucking hind tit.

10. Adapa,

    Make that 9.999.996…You forgot about the origins of new information…

11. J-Mac,

    Make that 9.999.995…You forgot about the origins of the first replicating molecule…

12. J-Mac:
    Adapa,

    Make that 9.999.997…You forgot about the origins of information…

    9,999,998. Biological information comes from the interaction of random genetic variations with the environment.

    ID-Creationist FAIL.

13. LOL! Keep posting. The IDiot score is still stuck at 0.

14. J-Mac,

    Make that 9.999.994…You forgot about spontaneously forming proteins…

15. IDiot score still stuck at 0. But do keep highlighting how worthless ID-Creationism really is.

16. Adapa,

    If you don’t understand what the word origin means I suggest you don’t discuss subjects beyond your comprehension….;-)

    Nice chatting with you …Goodbye!

    BTW: You and mister foamy GD are on ignore now so you can start wasting your energy as of…now! lol

    Correction! Mr foamy GD is on ignore for few days now… but please do not discourage his from writing his poetry…lol

17. Make that 9.999.993… You forgot about how bananas fit so well into our hands

18. dazz:
    Make that 9.999.993… You forgot about how bananas fit so well into our hands

    Amazing how the IDiots think listing the things science doesn’t know yet somehow subtracts from the things we do know.

    Not surprising the IDiots suck at math as badly as they suck at science.

19. dazz:
    Make that 9.999.993… You forgot about how bananas fit so well into our hands

    Only if you want to believe it…the power of suggestion is very strong…

    “If you repeat a lie often enough, it becomes the truth.”- Joseph Goebbels

20. dazz,

    Remember one thing, that even if I list 9,999,992 things science can’t explain about evolution, it is not going to have any effect on people who have preconceived ideas about evolution…who don’t want to change their mind…

21. Adapa: Amazing how the IDiots think listing the things science doesn’t know yet somehow subtracts from the things we do know.

    Not surprising the IDiots suck at math as badly as they suck at science.

    Actually, it’s not that amazing, because most traditional religions have usually held that all of their answers are right, and the other religions’ answers are not. So all that you had to do to show that the other religions were false was to show that they failed at this or that point, and they supposed that this showed that they were right, regardless of whether or not they really explained anything at all.

    That’s what really shows ID to be religious in nature, and not science. They treat actual science as if it were religion, and try to show that it fails here or there. As long as they’re not making claims that are obviously wrong (mostly they are, but they don’t see it, due to various deficits in learning and/or thinking), they win because the other “religion,” science, doesn’t explain whatever. They think they have an explanation for everything, God, and if science doesn’t explain everything it’s flawed and thus useless, at least where they don’t like it.

    It’s thoroughly disingenuous in terms of good science, or in any other empirical endeavor. It’s really not an empirical endeavor for them, however, it’s a priori and religious, and (in their minds) all they have to do is shoot down the “competing religion” to feel that their religion has won. They’re oblivious to the efforts to actually learn things about biology, a trivial matter compared with their efforts to preserve their religious “truth.”

    Glen Davidson

22. “If you repeat a lie often enough, it becomes the truth.”- Joseph Goebbels

    But that doesn’t work here in matters of science (well, it works on some, clearly).

    At UD, it seems to be the ruling concept, if one that they will never acknowledge in their own minds.

    Glen Davidson

23. J-Mac, you said you don’t like reading. Do you honestly think you’re educated enough to evaluate scientific arguments?

    But perhaps more importantly, do you believe your “arguments” are novel at all? Hint: they’re not. Not even close. Don’t expect anyone to pay attention to this.

24. GD; Nice seeing your name next to my OP….unfortunately I decided not to waste my time and read your I’m sure quite poetic comments…However, do not get discouraged and keep reading my OPs…there is more to come soon…maybe you can learn something? On the other hand….ta ta for now…
    P.S. When you feel uptight do what I do when I used read you comments…
    https://youtu.be/FdghRwWfaOQ

25. J-Mac: Remember one thing, that even if I list 9,999,992things science can’texplain about evolution, it is not going to have any effect on people who have preconceived ideas about evolution…who don’t want to change their mind…

    Adapa: Amazing how the IDiots think listing the things science doesn’t know yet somehow subtracts from the things we do know.

    Not surprising the IDiots suck at math as badly as they suck at science.

    As almost invariably is the case with creationists, your problem is much more fundamental than not knowing shit about biology (not that I know much either)
    it’s that you don’t understand basic reasoning.

26. J-Mac:
    GD; Nice seeing your name next to my OP….unfortunately I decided not to waste my time and read your I’m sure quite poetic comments…However, do not get discouraged and keep reading my OPs…there is more to come soon…maybe you can learn something? On the other hand….ta ta for now…
    P.S. When you feel uptight do what I do when I used read you comments…
    https://youtu.be/FdghRwWfaOQ

    Smart way of ignoring me, Clever Hans.

    Glen Davidson

27. dazz:
    J-Mac, you said you don’t like reading.

    I don’t think I said that I don’t like reading…I said I have no patience to read long articles, comments and OPs…I was being polite when I wrote that…If I didn’t like reading, I wouldn’t be where I am today…

    Do you honestly think you’re educated enough to evaluate scientific arguments?

    You made me lough…What kind of education does one need to evaluate a scientific argument?

    But perhaps more importantly, do you believe your “arguments” are novel at all?

    I don’t care..As far as I know arguments become old or not useful when the argument they were used in the first place was refuted… but unfortunately they weren’t …so until then…

    Hint: they’re not. Not even close. Don’t expect anyone to pay attention to this.

    Just because you don’t like my arguments or what they expose, it doesn’t make them wrong…It’s a free world pal!…and free blog…for now…and I don’t force you to read my OPs…

28. J-Mac:
    dazz,

    Remember one thing, that even if I list 9,999,992things science can’texplain about evolution, it is not going to have any effect on people who have preconceived ideas about evolution…who don’t want to change their mind…

    You’d think after all this time the IDiots would realize the only way to win people over to their position is by providing their own positive evidence, not just blindly attack the sciences which support ToE. But no. Lying for Jesus is the only strategy they can comprehend.

29. J-Mac: If I didn’t like reading, I wouldn’t be where I am today…

    There’s an argument against reading.

    Or at least against reading primarily pseudoscience and bullshit, like J-Mac.

    Glen Davidson

30. J-Mac: You made me lough…What kind of education does one need to evaluate a scientific argument?

    oh dear…

31. dazz:

    J-Mac: You made me lough…What kind of education does one need to evaluate a scientific argument?

    oh dear…

    Not really a shock that he doesn’t know.

    Glen Davidson

32. J-Mac:

    What kind of education does one need to evaluate a scientific argument?

    A basic understanding of the subject matter to start. Instead we get IDiots too ignorant to realize how ignorant they are.

33. HarleyDavidson and King Agrippa,

    Thank you so much for reading my OP! However, I can’t see your comments, which I’m sure they are very lovely…I just hope that by reading my upcoming OPs about 15-18 of them for now, you will come to your senses…
    Best wishes! J-Mac 😉

    Peace and love!

34. Shouldn’t there be some kind of rule that an OP has to be at least coherent? I’m not sure how it could be enforced, but when it’s violated I definitely get annoyed.

    In my experience, endosymbiosis is generally advanced as an explanation for mitochondria and plastids, not other features of eukaryotes. So what’s the point of all the other crap?

35. dazz: oh dear…

    You are making a lot of assumptions rather than presenting arguments or evidence …I guess it takes more than what you got…

36. John Harshman:
    Shouldn’t there be some kind of rule that an OP has to be at least coherent? I’m not sure how it could be enforced, but when it’s violated I definitely get annoyed.

    In my experience, endosymbiosis is generally advanced as an explanation for mitochondria and plastids, not other features of eukaryotes. So what’s the point of all the other crap?

    He’s a Creationist. Since when have they needed a reason to shovel their ignorance based anti-science bullcrap?

37. John Harshman: Shouldn’t there be some kind of rule that an OP has to be at least coherent?

    That’s what IDiots call censorship.

    Glen Davidson

38. J-Mac: I guess it takes more than what you got…

    That’s absolutely true, because I’m not arrogant enough to pretend that I understand this stuff all that well.
    There’s not much of a connection between endosymbiosis and religious beliefs (or lack thereof) anyway. Why the obsession with it? Couldn’t endosymbiosis have happened by the grace of God?

39. Endosymbiosys doesn’t explain the differing protein synthesis initiation in prokaryote vs. eukaryote. This is technical, but that’s where the absurdity of endosymbiotic theory as an explanation starts to be evident.

    You can zoom in here:

    https://liarsfordarwin.files.wordpress.com/2017/05/prokayote_protein_synthesis_initiation.png

    In the next comment I’ll show the eukaryotic protein synthesis initiation.

40. Below is the eukaryotic protein synthesis initiation which is in stark contrast to the prokaryotic protein initiation in the previous comment above.

    You can zoom in here:
    https://liarsfordarwin.files.wordpress.com/2017/05/eukaryote_protein_synthesis_initiation1.png?w=604

    For starters, the Shine Dalgarno sequence isn’t normally present in Eukaryotic DNA even for homologous genes, not to mention before the mRNAs are formed, eukaryotic genes homologous to prokaryotic genes have to have their spliceosomal introns spliced out.

    Next, it is readily apparent the initiation complexes and sequence of steps are different. If eukaryotes evolved from prokaryotes or if both evolved from a common ancestor, then how did changes in life critical steps emerge without killing the organism? Clearly there are life critical parts. The prokaryotic initiation is simpler, so how did the more complex eukaryotic system evolve.

    First notice the different order of the IF-3 (Initiation Factor 3) and IF-1 (Initiation Facotr 1) factors binding to the E and A location on the 30S subunit vs. the eIF1, eIF3, and eIF1A binding to the E, P, A locations on the 405 subunit.

    How did that proceed from a common ancestor since this sort of re-ordering, if not done in concert with other simultaneous changes would be lethal.

    I could go one and on, but hopefully the reader gets the picture! 🙂

    These are some of the reasons I find God and miracles a better explanation. Why? It is clear even assuming the doctrine of common descent that miraculous transformations are necessary for common descent to be true. But if one invokes miracles, one is essentially a creationist already.

41. stcordova: Next, it is readily apparent the initiation complexes and sequence of steps are different. If eukaryotes evolved from prokaryotes or if both evolved from a common ancestor, then how did changes in life critical steps emerge without killing the organism? Clearly there are life critical parts.

    By adding one part at a time and making it necessary?

    How did the designer design and make them? *POOF* and there they all were, fully formed?

    The prokaryotic initiation is simpler, so how did the more complex eukaryotic system evolve.

    Gradually, one component at a time?

    First notice the different order of the IF-3 (Initiation Factor 3) and IF-1 (Initiation Facotr 1) factors binding to the E and A location on the 30S subunit vs. the eIF1, eIF3, and eIF1A binding to the E, P, A locations on the 405 subunit.

    How did that proceed from a common ancestor since this sort of re-ordering, if not done in concert with other simultaneous changes would be lethal.

    First of all it’s important to understand that the evolution of the modern eukaryotic process of transcription and translation did not evolve from the modern prokaryotic process of transcription and translation.

    So if both processes look like it might be hard to derive one directly from the other (as it would require what looks like lethal rearrangements), that could simply be an artifact of the fact that they didn’t, but instead both evolved from a common ancestor.

    I could go one and on, but hopefully the reader gets the picture!

    These are some of the reasons I find God and miracles a better explanation. Why?

    Yes, why? You can explain everything with that. Literally. There is nothing we could observe, even in principle, that you could not just declare was what God wanted to design.

    It is clear even assuming the doctrine of common descent that miraculous transformations are necessary for common descent to be true.

    So in order to avoid what you see as a “miraculous” transformation (many small steps), you instead posit… a literal miracle. (Whole goddamn thing at once, in an instant).

    How the hell does that make it more plausible?
    Does not compute.

    Your reasoning seems to be something like this:
    Nobody can show me all the small steps by which this happened. And if they did, I’d call it a “just so story”. So if there’s not good enough evidence to show all the small steps it happened by, it would have to happen by a giant leap.
    But giant leaps are extremely unlikely. So instead I now believe it happened by the biggest possible leap of all. Because of another just so story I will never be able to experimentally test.

    The word irony becomes pertinent.

42. stcordova,

    Below is the eukaryotic protein synthesis initiation which is in stark contrast to the prokaryotic protein initiation in the previous comment above.

    Sure, there are many differences between eukaryotes and prokaryotes. But there is a basic logic error here. You seem to assume that, if an evolutionary transition occurred, it should have left descendants of every intermediate stage, so that we can reconstruct the sequence. If no such intermediates can be found, it happened all at once, and therefore couldn’t have happened unaided.

    Clearly, that is fallacious.

43. Why can’t God generate a space of possibilities that is connected by small steps, I wonder? Is he a bit limited?

44. If God did it, He took an alpha-proteobacterium and shoved it inside an archaeon. Then did it again with cyanobacteria in plants. And again with secondary and tertiary endosymbionts – nested Russian dolls of engulfment, all membranes retained.

    And there is no way that that process could have happened ‘naturally’? Why?

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

    Just a bit.

46. J-Mac,

    Will these very facts overturn the evolutionary thinking and bring down the theory of evolution? One would hope… but of course not…

    Until an alternative theory is proposed that explains all the current observations and more then we’ll stick with evolution. So far you have proposed no such alternative, unless “it was designed” is it?

    J-Mac: Make that 9.999.997…You forgot about the origins of information…

    I must have missed the true origin of information according to ID. What is it?

47. First notice the different order of the IF-3 (Initiation Factor 3) and IF-1 (Initiation Facotr 1) factors binding to the E and A location on the 30S subunit vs. the eIF1, eIF3, and eIF1A binding to the E, P, A locations on the 405 subunit.

    I’m not convinced the order of binding is that substantially different. In eukaryotes eIF2 binds tRNA before tRNA binds the small subunit, and in prokaryotes eIF2 binds tRNA after tRNA has bound the small subunit. Doesn’t look like a miraculous transformation to me.

    Also the different factors are named differently, but eIF1 from eukaryotes actually is homologous to IF-3 from prokaryotes, just as IF-1 from prokaryotes is homologous to eIF1A in eukaryotes.

    The names do not specify the order of binding, nor the relationship between prokaryotes to eukaryotes. And the more I look at those two diagrams, the more obvious the commonalities become. Eukaryotes basically just look like they have more steps added on.

    There are also examples known of cap-independent translation in eukaryotes (where apparently the eIF4F factor shown in your diagram isn’t needed). Which brings up an important point, as even within eukaryotes and prokaryotes, there are differences in the processes of translation and transcription.

    Having two diagrams like these make it seem like this is what happens in ALL cells from eukaryotes and prokaryotes under ALL circumstances, and that everything we see is critical and life couldn’t exist without it. Yet that is very rarely the case in biology. There are exceptions known to some of these steps. Some viruses even “deliberately” attack and inhibit some of the normal steps in eukaryotic translation, as this will inhibit normal cellular translation, but the virus’s own genes can still be transcribed and translated without some of the normally required factors. Needless to say, viruses don’t have introns, which in turn goes to show that these systems can function without “all of it present”.

    A related point is I wonder how similar bacterial transcription is to archaeal transcription.

48. OMagain: Just a bit.

    Hahaha, that TV-show is fucking brilliant and insane.

49. stcordova,

    How much explanatory power does ‘it’s a miracle’ really have? For example –

    Why is the mitochondrial initiation system more closely related to that of prokaryotes than to that of the nucleus? Why do mitochondria of the slime mold Physarum polycephalum need a unique DNA condensation factor that can nonetheless complement E. coli deficient in ‘histone-like’ factor HU?

    Yeah, details, details. But, I’m only doing what Creationists do.

50. stcordova: Below is the eukaryotic protein synthesis initiation which is in stark contrast to the prokaryotic protein initiation in the previous comment above.

    Couldn’t we at least drop the term “prokaryote”, in favor of the three-domain nomenclature? Many features of cell biology, including translation initiation, are radically different between archaea and bacteria. I guess the “prokaryotic” translation initiation process depicted is from bacteria, right?
    Doesn’t the archaean translation initiation process involve several more proteins homologous with eukaryote ones?