On the Origin of Mitochondria: Reasons for Skepticism on the Endosymbiotic Story

_{Jonathan McLatchie

January 10, 2012

Intelligent Design}

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With regret, ENV recently noted the passing of biologist Lynn Margulis. Margulis, a scientist whom I admired greatly, was never a stranger to controversy, going so far as to call neo-Darwinism “a complete funk” and asserting that “The critics, including the creationist critics, are right about their criticism. It’s just that they’ve got nothing to offer by intelligent design or ‘God did it.’ They have no alternatives that are scientific.” She was a scientist who wasn’t afraid to think creatively, disregarding the scorn of her colleagues. According to the Telegraph, a response to one grant application she made said: “Your research is crap. Don’t ever bother to apply again.”

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Comments

Well if common descent can’t explain the other differences then it can’t explain anything.
"The other differences?". Say we focus on ONE gene and look for the signal of common descent. And find it. In finding it, we have not even been looking at "the other differences". And therefore have failed to explain anything? You'll say anything for a laugh. I'm going to adopt your new habit of bolding. Common descent hypothesises that two sequences descend from a common ancestor. It does not say anything about the causes that impinged upon the lives of the organisms or their ancestors. If you have commonality in two sequences, your hypothesis of common descent stands firm. If you determine commonality in other sequences, your hypothesis is bolstered; if you don't, it is weakened.
You can’t say “common descent is the only explanation for X” when you don’t even know if common descent can account for X.
You continue to confuse the mechanisms of evolution - selection and drift - with the simple consequence of individuals or populations having more than one descendant - common descent. If there are two surviving descendants of sequence X, they are commonly descended. Common descent does not need to 'account for' the two descendant X's; it is enough that they exist. It is entirely possible that one sequence says AAAAA and the other says GGGGG. They are still commonly descended, but the sequences are completely uninformative of that fact. Alternatively, if the sequences both say AAAAA, this is supportive (though not conclusively) of the hypothesis of common descent.
And when have we observed fixation?
Whenever rare alleles become extinct
And when have accumulations of random mutations been observed to construct any multiprotein configuration?
What has that to do with the price of fish? Sequence analysis is about the DNA, not about the proteins built from it and their evolution.
If you are referring to sex, you need to bear in mind that, once a mutation is fixed in the population, all descendants will have it. Until they lose it
Hmmmmm ..... yeeeessss... until they lose it .... and then all subsequent descendants will have that 'loss'. Both presence and absence can be used as markers. AGyA begets AGxA begets AGxA begets AGxA begets AGA begets AGA begets ...
Also you don’t seem you understand a nested hierarchy. Population A does not consist of nor contain A1, A2 and A3.
Ye gods! I don't understand nested hierarchies! No, until it has actually had descendants, A does indeed not give a nested hierarchy. Sigh. The nested hierarchy is obtained by examination of the twigs - A1, A2 and A3 - and allocation to sets on the basis of shared characters. Sequences common to A1 and A2 and A3 group A1, A2 and A3 together. Sequences common to A1 and A2 but not A3 group A1 and A2 together. This hierarchy is nested. Set A1/A2 fits inside A1/A2/A3 like a little Babushka doll. The Venn diagrams drawn on the basis of the shared genes do not cross. This is the 'ideal' - the expectation against which hypothetical relationships are tested: constructing the tree with the fewest changes and no overlap. Obviously, this expectation is not always precisely met, for various reasons.Chas D_{January 12, 2012
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Chas D:
Doesn’t matter – any sequence retained can be used to try and construct a tree.
We can construct a tree based on a common design.
Whatever ‘other’ differences may exist, and their explanation, are independent matters.
Well if common descent can't explain the other differences then it can't explain anything. You can't say "common descent is the only explanation for X" when you don't even know if common descent can account for X.
Fortunately, the observed processes of speciation and mutation-fixation (mutation and subsequent fixation by drift and selection) suggest otherwise.
And when have we observed fixation? And when have accumulations of random mutations been observed to construct any multiprotein configuration? BTW a family tree doesn’t produce a nested hierarchy.
Yes, it does.
Wrong- ya see I am a member of several family trees and that is not alowed in a nested hierarchy.
If you are referring to sex, you need to bear in mind that, once a mutation is fixed in the population, all descendants will have it.
Until they lose it- and when has muational fixation been observed? That is the problem- with evolution it is whatever works- no progress. Also you don't seem you understand a nested hierarchy. Population A does not consist of nor contain A1, A2 and A3.Joe_{January 12, 2012
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Universal common descent does not explain non-functional parts staying intact over many, many generations so it can used as a genetic marker.
It does not need to. You seem to think there are only two kinds of common descent - universal and 'local'. You are correct; it is highly unlikely that nonfunctional sequences will be preserved in all organisms from LUCA. But I'm not talking about universal descent. You keep sticking 'universal' in front and I keep knocking it off. For resolving less deep branches within the tree, retention of nonfunctional DNA is entirely within the bounds of expectation. Degradation of DNA is a stochastic process, influenced by selection. Nonfunctional DNA is expected to degrade at the 'background' rate - degradation at that rate is a pretty good reason to declare it nonfunctional. The SINE inserts mentioned in the discussion on whale phylogeny are perfectly capable of identifiable recovery within the timescale they are used to probe (50-60 million years ago). If they weren't, people wouldn't be publishing papers on them. You think people who investigate phylogenetic analyses don't understand their own subject?
Non-functional similarities do not explain all the differences observed.
Doesn't matter - any sequence retained can be used to try and construct a tree. Whatever 'other' differences may exist, and their explanation, are independent matters.
For universal common descent to have any explanatory power at all you need something to account for all the physiological and anatomical differences observed. And science falls far short of that.
It suffices that its signal is observed and capable of analysis. Accounting for the differences is not the job of phylogenetic analysis.
Humans give rise to humans, finches give rise to finches, fish give rise to fish and there isn’t anything to say that will ever change.
Biodioversity is stuffed, then. Fortunately, the observed processes of speciation and mutation-fixation (mutation and subsequent fixation by drift and selection) suggest otherwise.
BTW a family tree doesn’t produce a nested hierarchy.
Yes, it does. If you are referring to sex, you need to bear in mind that, once a mutation is fixed in the population, all descendants will have it. Speciation at population level is an 'asexual' process, and does produce a nested hierarchy - fixed alleles in population A will be copied into all descendant species A1, A2, A3. Alleles fixed in A1 after divergence will be seen in A1a and A1b but not in A2 or A3.Chas D_{January 12, 2012
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Universal common descent does not explain non-functional parts staying intact over many, many generations so it can used as a genetic marker. Non-functional similarities do not explain all the differences observed. For universal common descent to have any explanatory power at all you need something to account for all the physiological and anatomical differences observed. And science falls far short of that. Humans give rise to humans, finches give rise to finches, fish give rise to fish and there isn't anything to say that will ever change. BTW a family tree doesn't produce a nested hierarchy.Joe_{January 12, 2012
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Borrowing greatly from talk origins, again:
Trying to explain, again ... the 'design relationship' you invoke relates to a kind of 'blueprint' view of life. Certainly, commonality among the functional parts of such 'blueprints' could be ascribed to design requirements. But the nonfunctional parts? Why do they follow the same pattern given by the functional parts? They don't need to from a design point of view. But they do. The correspondence of nonfunctional parts with the functional phylogeny is NOT explained by a 'common design requirement'. There is no design requirement in the nonfunctional parts - lack of requirement is what makes them nonfunctional. So the only "designed" non-descent explanation for these trees of nonfunctional DNA is a deliberate attempt to mislead. If two independent lines appeared without ancestors, this discontinuity has been papered over to appear indistinguishable from a continuum of descent. Only those furnished with special ID goggles can see it. Amongst DNA observed to descend from a common origin, common descent is the correct explanation. Amongst artificial datasets computer-generated to test methods of phylogeny recovery from natural datasets, again common descent is the correct explanation. And we can use those methods, tested against artificial descent phylogenies, and miraculously recover trees from real phylogenies, as if they were descent phylogenies. I wonder why.
That said the design inference is based on our knowledge of cause and effect relationships. It is your position that relies on ignorance and promissory notes.
Baloney. We have a cause and effect relationship between a replicating population and the pattern of inheritance in descendants. That is, indeed, a direct relationship between the phenomenon and its known effects, rather than some vaguely inferred extension from machine design to the biological. We also have a cause and effect relationship between finite populations and the survivorship of ancestry within those populations. Again, that is a direct relationship between the phenomenon and its consequences, not some vague analogy, and it leads to a testable expectation of coalescence. There may be limits. But they do not manifest themselves in phylogenetic analysis. There is no a priori reason to suppose that phylogenies deriving from cryptic ancestors are constructed in a fundamentally different way from those deriving from observable ones, given that there is no obvious discontinuity between species-level and (say) family-level relationships. Newtons First Rule and all that.Chas D_{January 12, 2012
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Joe, there are numerous experiments that can be done to demonstrate common descent. If common descent is real, we would expect the physical differences between recent ancestors to be less than between a recent ancestor and a distant ancestor. The fossil record has many examples of this. We would also expect the DNA between recent ancestors to be closer than between a recent and a distant ancestor. DNA research has shown this every time that it is looked at.Ken_M_{January 12, 2012
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Chas, There is no way to take common descent and extrapolate universal common descent. Only imagination can do that. That said the design inference is based on our knowledge of cause and effect relationships. It is your position that relies on ignorance and promissory notes.Joe_{January 12, 2012
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Really? We observe the universality of a designer’s involvement in every nook and cranny of the Tree/Web of life? How so?
Borrowing greatly from talk origins, again: According to the theory of common design, modern living organisms, with all their incredible differences, are the progeny of one single design standard in the distant past. In spite of the extensive variation of form and function among organisms, several fundamental criteria characterize all life. Some of the macroscopic properties that characterize all of life are (1) replication, (2) heritability (characteristics of descendents are correlated with those of ancestors), (3) catalysis, and (4) energy utilization (metabolism). At a very minimum, these four functions are required to generate a physical historical process that can be described by a phylogenetic tree. If every living species designed according to an original standard that had these four obligate functions, then all living species today should necessarily have these functions (a somewhat trivial conclusion). Most importantly, however, all modern species should have inherited the structures that perform these functions. Thus, a basic prediction of the design relatedness of all life, combined with the constraint of gradualism, is that organisms should be very similar in the particular mechanisms and structures that execute these four basic life processes. and common descent (without the universal) is baraminology.
And ID is not creationism?
Non-sequitur. I was just making a point.Joe_{January 12, 2012
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Universal common design is observed
Really? We observe the universality of a designer's involvement in every nook and cranny of the Tree/Web of life? How so?
and common descent (without the universal) is baraminology.
And ID is not creationism?Chas D_{January 12, 2012
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Why are nonfunctional elements consistent with universal common descent?
Well (dropping the 'universal' bit) because when we look at assumed nonfunctional elements - eg karyotype rearrangements, silent substitutions etc - we can reconstruct nested clades. Such a phylogeny is a prediction of inheritance with branching. You might just about get away with design constraints to explain relationships in functional parts of designs. But there is no sound reason for nonfunctional parts of a design to follow an apparent phylogeny beyond whim, or deceit, or hidden purpose. One way out of that for the determined design advocate is to deny that they are nonfunctional. That way, you can say that everything explained by common descent is also explicable by common design. But if you accept that some latitude exists in nonfunctional elements, then their commonality/difference, on the design hypothesis, is not attributable to a fundamental requirement of the designs. And yet it follows the same pattern as the functional part of the design. It isn't a design constraint, and it looks for all the world like common descent. What the hell are we to say it is, then? We can't say common descent because it would expose us as materialist ideologues? Ho ho.
ID does not start with the designer did it. ID starts with we don’t know and goes from there.
ID starts from we don't know and stays there.
As I said we have direct observational evidence of common design. All we for universal common descent is imagination.
And as I said, you are being selective with your qualifications. We have direct observational evidence of common descent. Look up paternity testing, or family trees of genetic defects, or familiarise yourself with the means by which organisms come into existence and perish. This precise process is extrapolated back into the past. What is illegitimate about that, I do not know - it is exactly the same process, operating on exactly the same entities (contra your instances of complex design). If I had a parent, and my parents had parents, and they had parents ... Yes, I need to imagine that process carrying on backwards. It's not that hard. It is the same process: generational inheritance with branching (or in reverse: with confluence).
So what do you have beyond pleading?
You're never, ever going to 'get' common descent, are you? Perhaps biology is not for you.Chas D_{January 12, 2012
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Universal common design is observed and common descent (without the universal) is baraminology.Joe_{January 12, 2012
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Why are nonfunctional elements consistent with universal common descent?
Common design would demand that every last detail of the common elements be functional in both examples being compared.
No it wouldn't. ID does not start with the designer did it. ID starts with we don't know and goes from there. As I said we have direct observational evidence of common design. All we for universal common descent is imagination. So what do you have beyond pleading?Joe_{January 12, 2012
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Again common design is observed and universal common descent is only imagined.
Craftily phrased. Common descent is observed. Universal design is not.Chas D_{January 12, 2012
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Chas: “IF mitochondria were bacteria, what molecular, structural or physiological features are consistent with this hypothesis? Which aren’t?” Joe: Right, “it looks like”.
No, really, no. You START with some kind of simplistic position like "looks like". Then you drill down to multiple independent lines of evidence. You didn't know you were going to find further similarity, but each time you do, your hypothesis is further supported. If you start with the position "designdidit", everything you find is consistent with that position. Why even bother looking? Of course, the resemblance of many, many features to free-living bacteria requires the special-pleading extension: "designdiditbyborrowingsomefeaturesfrombacteria". Which, to my mind, is an extra layer not warranted, and not supported by or distinguishable via any feature of the system. You might as well go for "created last Thursday".
As I said I can take your evidence for universal common descent and make a strong case for common design- same type of tests, except common design is actually an experienced and observed phenom, using the same evidence. Must mean common design is scientific…
Common design would demand that every last detail of the common elements be functional in both examples being compared. Parallel commonality in nonfunctional elements is only ascribable to Designer's Whim, or Hidden Purpose, in that scenario. I really don't know why a designer would go to the trouble of trying to fool biologists. Guess it's all part of the plan. So, do you assert that every piece of DNA in every organism on earth is functional? Yes? How come we see variation in species? How come we can mess with DNA with no effect? Silent substitutions, inserts and excisions and other discontinuities in DNA, viral insert 'scars', karyotype and every last element of morphology - all of these are functional? No? Why are these 'designed' nonfunctional elements consistent with common descent? What is the Designer trying to do to our heads?Chas D_{January 12, 2012
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OK Art, some bacteria with a linear chromosome are pathogenic. And there is a paper (or more) that discusses this- that endosymbiosis wasn't necessarily the voluntary engulfing of a smaller prokaryote for food, rather it was the invasion of larger prokaryote by a smaller pathogenic prokaryote that started the relationship. Touche. Sorry Jonathon...Joe_{January 11, 2012
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Endosymbiosis is an ongoing process. Google "Jeon symbiosis" for some interesting pointers.Arthur Hunt_{January 11, 2012
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Some of what I'm talking about: http://www.pnas.org/content/100/15/8828.long http://www.plantcell.org/content/18/11/2869.longArthur Hunt_{January 11, 2012
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There almost is always going to be intermediate stage where the gene will be present in both genomes. That gives the cell a chance to evolve to control a copy from the nucleus without losing the function in the mitochondria. Check out Carsonella Ruddii: http://en.wikipedia.org/wiki/Candidatus_Carsonella_ruddii. Its a sequenced genome that is somewhere on the path between obligate symbiont and organelle.Starbuck_{January 11, 2012
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Chas D:
“IF mitochondria were bacteria, what molecular, structural or physiological features are consistent with this hypothesis? Which aren’t?”.
Right, "it looks like". Common design is an observable phenomenon that accounts for "looks like".
“IF organisms are related by descent, what patterns would we expect to see in morphology or karyotype or gene sequence or protein structure among hypothetically related groups? What else might explain them? How could we test that?.
Again common design is observed and universal common descent is only imagined. Ya see Chas there aren't any experiments in which we can test endosymbiosis wrt becoming mitochondria. And there isn't any way to test universal common descent- we have no idea if the transformations required are even possible. We can't go into a lab, take some fish and their embryos, get the embryos to mutate- or even specifically target areas for muation- and get a fish that develops limbs strong enough to enable it to walk on land. It is all circumstantial evidence which is directly influenced by personal biases. As I said I can take your evidence for universal common descent and make a strong case for common design- same type of tests, except common design is actually an experienced and observed phenom, using the same evidence. Must mean common design is scientific...Joe_{January 11, 2012
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the movement of genes from organellar to nuclear genome
And even from cytoplasm-resident bacteria (that themselves get into cells via a mechanism!)Chas D_{January 11, 2012
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Arthur Hunt:
Um, Jonathan, you do know, don’t you, that bacteria have linear chromosomes...
So endosymbiosis was an ongoing process involving different types of bacteria- is that the inference? Just asking.Joe_{January 11, 2012
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It is strange that on one hand evos chide ID as saying the “evidence” for ID is nothing more than “it looks designed”. Yet the “evidence” for endosymbiosis as the origin of mitochondria is “mitochondria look like bacteria” and the evidence for UCD is “it looks like common descent” or “it looks like evolutiondidit”. Anyone else notice this?
The reasonaing is taken a tad further than that! Once the hypothesis is advanced, one devises various ways to test it - "IF mitochondria were bacteria, what molecular, structural or physiological features are consistent with this hypothesis? Which aren't?". "IF organisms are related by descent, what patterns would we expect to see in morphology or karyotype or gene sequence or protein structure among hypothetically related groups? What else might explain them? How could we test that?. The hypotheses have so far been amply confirmed by the evidence gathered to date - thousands and thousands of papers. Which is astonishing, as they are such patent hogwash. Oh hang on, maybe they aren't.Chas D_{January 11, 2012
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It is strange that on one hand evos chide ID as saying the "evidence" for ID is nothing more than "it looks designed". Yet the "evidence" for endosymbiosis as the origin of mitochondria is "mitochondria look like bacteria" and the evidence for UCD is "it looks like common descent" or "it looks like evolutiondidit". Anyone else notice this?Joe_{January 11, 2012
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Um, Jonathan, you do know, don't you, that bacteria have linear chromosomes, that bacterial genes have introns that are removed without the help of anything that resembles the eukaryotic spliceosome (with one tantalizing exception), and that the movement of genes (as well as their "activation") from organellar to nuclear genome can be detected and studied in real time?Arthur Hunt_{January 10, 2012
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