The Mysteries of Evolution: 2. The Origin of Life and the miserable failure to reassemble Humpty Dumpty

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Not much can be written after you watch the two videos above…

It is pretty easy to understand for those who choose to understand that the theory of abiogenesis and the probability of life spontaneously self-assembling is just a science-fiction story to fill the void for those who need to believe in something other than the obvious…

If the living cell can’t be reassembled in a lab, what evidence is there that life spontaneously self-assembled other than in science-fiction stories?

Now, let’s listen to the excuses…

231 thoughts on “The Mysteries of Evolution: 2. The Origin of Life and the miserable failure to reassemble Humpty Dumpty”

  1. colewd: Until we have a mechanism that can move from functional DNA of animal A to functional DNA of animal B where new genes and capabilities are formed then it looks like a creation event.

    What a colossal failure of logic.

    If we lack a mechanism for how A turns into B, then we lack a mechanism. It doesn’t mean something is correct by default.
    NOTHING is correct by default, ALL hypotheses require evidence to substantiate them beyond conjecture.

    The mere fact that A and B exists doesn’t mean we can automatically conclude they were created.

    Only a few hundred years ago we had no ideas how any of the elements form. Should we then have believed they were created by fiat? That’s ridiculous. If we don’t know, then we don’t know. The answer isn’t “oh gee then I guess a wizad musta dunit”.
    Turns out the elements come to exist through various nuclear fusion and fission reactions.

  2. colewd: Here is an example of a fish and environment where an oxygen carrying protein is not required. Note that the conditions are very cold and the fish has lots of veins and arteries. The claim here is that the efficiency is 10% of a system with an oxygen transporting protein.

    I would honestly expect binding of molecular oxygen to be ubiquitous. Oxygen probably weakly associates with the surfaces of all water-soluble proteins.

    You just have to know a tiny bit of basic organic chemistry and you can glean from first principles how the evolutionary process occurs at the molecular level.

    You really should take some basic organic chemistry. Don’t start with biochemistry, just start with organic chemistry. Learn to draw, recognize and name bonds, functional groups and basic organic molecules like alkanes, alkenes, alkynes, alcohols and so on. Learn about intermolecular binding, Vand Der Waals forces, electronegativity, polarity and the whole shebang. It’s actually not that complicated. This basic knowledge will put the whole of biochemistry and molecular biology in a totally different light and you will start to understand how proteins bind and interact with each other, something about how they fold and so on. Supplant the basics with basic protein biochemistry, like primary, 2ndary, tertiary and quaternary structure of proteins. Go on to pKa values and solubility etc etc.

    These things you think are so mysterious and impossible for a “random process” to achieve really just aren’t. I don’t know what else to tell you here, but you lack understanding of the basic principles.

  3. colewd: Until we have a mechanism that can move from functional DNA of animal A to functional DNA of animal B where new genes and capabilities are formed then it looks like a creation event.

    Why is your belief exempt from the requirement for evidence?

    It looks to you like a creation event, because you think that creation is the default “explanation.” But you don’t and haven’t explained anything about life, ever. I think it’s fair to say that you have no explanation and do not want any, for you wish to believe something that utterly lacks the first bit of evidence that could give anyone a reason to believe it. No one really minds your blissful ignorance, of course, but that you try to portray it as superior knowledge is misleading to anyone with as little understanding of the standards necessary for actual discovery.

    Glen Davidson

  4. Kantian Naturalist,

    Indeed, so you keep saying. But apart from an expression of personal incredulity, no arguments have been forthcoming for this claim. And personal incredulity has no epistemic significance.

    The argument is that the ways to arrange DNA to create a protein function are less then the ways that do not. As proteins become more complex this problem gets worse. Random change will cause a protein to drift away from function. This is avoided by repair mechanisms inside the cell however these mechanisms reduce the variation which is a head wind for evolution.

    Johns counter argument that occasionally advantageous mutations will find survival improvements is correct but there is no evidence that these changes can result in a complex organ or group of organs that are the make up of multicellular organisms.

  5. Rumraket,

    If we lack a mechanism for how A turns into B, then we lack a mechanism. It doesn’t mean something is correct by default.
    NOTHING is correct by default, ALL hypotheses require evidence to substantiate them beyond conjecture.

    Should this same standard be applied to evolution?

  6. colewd: Should this same standard be applied to evolution?

    Sure. Are you saying there is no evidence for biological evolution?

  7. colewd: Johns counter argument that occasionally advantageous mutations will find survival improvements is correct but there is no evidence that these changes can result in a complex organ or group of organs that are the make up of multicellular organisms.

    Heh, so near yet so far.

  8. colewd: Random change will cause a protein to drift away from function. This is avoided by repair mechanisms inside the cell however these mechanisms reduce the variation which is a head wind for evolution.

    You keep bringing up repair mechanisms, I keep pointing out that known mutation rates include the action of repair mechanisms, and you keep ignoring the correction. No, what keeps proteins from drifting away from function is natural selection acting against deleterious mutations.

    Johns counter argument that occasionally advantageous mutations will find survival improvements is correct but there is no evidence that these changes can result in a complex organ or group of organs that are the make up of multicellular organisms.

    I’d say there’s plenty of evidence, since species differ by exactly the sorts of differences we see arising by mutation, and they are clearly connected by common descent. It’s also clear that complex organs have arisen gradually, as is shown by mapping of traits onto phylogeny. You just refuse to think about the evidence.

  9. colewd: Should this same standard be applied to evolution?

    Yes. Obviously. And it IS applied to evolution. You just don’t understand what evidence is. You don’t understand how phylogenetics is based on actual evidence.

  10. colewd,
    Do you think the continents drift? Why? Have you ever observed them do such?

  12. OMagain,

    Do you think the continents drift? Why? Have you ever observed them do such?

    Continents do not have DNA to organize into functional code that can build a complex animal. The hypothesis that this can happen through random change supported by selection once new function is reached is not well supported by experimental science.

    The bacterial flagellum irreducible complexity counter arguments are a good example of this.

    The macro machines unique to the eukaryotic cell (spliceosome nuclear pore complex) are more complex (measured by number of proteins and number or nucleotides to support) then the flagellar motor.

  13. Rumraket,

    Yes. Obviously. And it IS applied to evolution. You just don’t understand what evidence is. You don’t understand how phylogenetics is based on actual evidence.

    This is a silly statement. We both know what evidence is. I understand that there is similar biochemistry throughout life and I also see that this is supporting evidence of common descent yet without strong evidence of how the transitions occurred it is inadequate to explain the theory.

    The paper that John wrote has birds losing flight multiple times in order to support the UCD hypothesis. The paper Koonin wrote had 2400 eukaryotic genes without prokaryotic homologs.

    When are you guys going to face the contradictory evidence to the UCD hypothesis?

  14. John Harshman,

    You keep bringing up repair mechanisms, I keep pointing out that known mutation rates include the action of repair mechanisms, and you keep ignoring the correction. No, what keeps proteins from drifting away from function is natural selection acting against deleterious mutations.

    I don’t think you have a good argument here that there are well established mutation rates.

  15. colewd: When are you guys going to face the contradictory evidence to the UCD hypothesis?

    When are you going to face the evidence that gave rise to idea of common descent (you’re still confused about UCD? Do you ever learn?).

    Contradictory evidence would be evidence that points toward a different cause, or that was incompatible with the proposed cause. What sort of evidence do you have of a different cause of the vast commonalities across life, including eukaryotes? What evidence do you have that is contrary to common descent? Continuity and change are what are expected from common descent. What about eukaryotes differs from that? In what manner does anything about eukaryotes point to any intelligent cause that can be identified or reasonably extrapolated from identified beings?

    Have you ever properly considered the explanatory value of common descent, as well as the utter vacuity of the “design hypothesis”? The evidence is that you have not. Of course the real problem is that you’re defending religion, not trying to understand biology, hence it matters not a whit to you that evolutionary theory explains vast amounts of data and ID truly explains none at all.

    Glen Davidson

  16. GlenDavidson,

    Contradictory evidence would be evidence that points toward a different cause, or that was incompatible with the proposed cause. What sort of evidence do you have of a different cause of the vast commonalities across life, including eukaryotes?

    The evidence of 2400 genes without homologs is pointing to a separate origin event. As a bird on an island thousand of miles away that cannot fly is pointing to a separate origin event.

  17. colewd: GlenDavidson,

    Contradictory evidence would be evidence that points toward a different cause, or that was incompatible with the proposed cause. What sort of evidence do you have of a different cause of the vast commonalities across life, including eukaryotes?

    The evidence of 2400 genes without homologs is pointing to a separate origin event. As a bird on an island thousand of miles away that cannot fly is pointing to a separate origin event.

    Shorter, no, you don’t have any evidence of a different cause.

    Incredulity regarding evolution, completely credulous regarding design.

    Glen Davidson

  18. colewd: As a bird on an island thousand of miles away that cannot fly is pointing to a separate origin event.

    For instance?

  21. colewd:
    Rumraket,
    This is a silly statement.We both know what evidence is.I understand that there is similar biochemistry throughout life and I also see that this is supporting evidence of common descent yet without strong evidence of how the transitions occurred it is inadequate to explain the theory.

    I still don’t think you know what “explain” means. Nor do you seem to know what evidence is, despite your claim, if you think that “similar biochemistry throughout life” is the supporting evidence for common descent.

    The paper that John wrote has birds losing flight multiple times in order to support the UCD hypothesis.The paper Koonin wrote had 2400 eukaryotic genes without prokaryotic homologs.

    You have no clue. My paper has nothing to do with the UCD hypothesis. The tree supports multiple losses of flight, not the other way around.

    When are you guys going to face the contradictory evidence to the UCD hypothesis?

    What’s your alternative? Does the evidence support your alternative better than it supports common descent? You’re cherry-picking again. What’s harder to believe, several losses of flight or independent hierarchical DNA sequence similarities in 18 genes? What’s harder to believe, common descent because of 3500 genes with homologs or separate creation because of 2400 genes without homologs?

    And I point out once more, in utter futility, that you have never explained what you think was separately created and what shares descent. Is each bird species a separate creation, or are some birds related? Is each eukaryote species a separate creation or are eukaryotes just separate from prokaryotes? Your implied positions (never actually stated) are mutually contradictory.

    As a bird on an island thousand of miles away that cannot fly is pointing to a separate origin event.

    Or perhaps it points toward loss of flight. How would you tell the difference? (I can suggest ways if you can’t.)

  23. colewd: You always have the birds ancestor built a raft hypothesis.

    I prefer the unknown designer did something somewhen somewhere hypothesis, personally.

  24. OMagain,

    I prefer the unknown designer did something somewhen somewhere hypothesis, personally.

    Mysterious designers are interesting. 🙂

  26. John Harshman:

    CharlieM: So showing the intermediate steps can exist does not, of necessity, show that the configuration of the former in the series is the cause of the configuration of the latter. There are other explanations, as demonstrated in the case of buttercup leaves.

    Quite true, stripped of the meaningless mysticism.

    Goethe did not indulge in meaningless mysticism. As Brady notes:

    Goethe had read various speculations concerning a “vital force” which would account for the realm of life, but he thought it to be an obscure explanation, borrowed from mechanical habits of thought and made redundant by what we actually know about life. The parts of an organism, for example, are no more separable from their context than is the entire animal — they are all equally alive. Such parts, singly or collectively, are continually transformed by development, and are but a partial disclosure of that development at any point in time. They are, as parts, inseparable for the potential-to-be-otherwise that constitutes becoming, for if we think of them without this we think them out of context — they lose their identity and their intelligibility. (Corpses, as I have already noted, make sense only by reference to the generative mode from which they came.) On the other hand a “force” in the mechanical sense of the term is quite separable from the object to which it may be applied, and the affected object is in existence prior to that application and sometimes after its cessation. The objects of a separable force are not made, but simply moved, by the force. The parts of an organism owe their very existence to their potency. In order to exist at all they must be potent (corpses must have been potent) and do not need the addition of another power to make them change

    For Goethe, talk of a vital force was a needless and misleading speculation.

    John Harshman:
    The point of intermediate forms is to show that transformations are plausible, though Bill claims they are not. It’s the nested hierarchy of life and its fit to the fossil record that show descent, hence transformation.

    So in the case of the butterfly leaves you agree that each leaf in the series is not a copy from the previous leaf which has been slightly altered. But in the case of sections of DNA or of proteins you do believe that this is the case. Because of their similarity you assume that one must be derived from the other by some sort of accidental duplication.

    Brady continues:

    Turning to modern morphology we find, of course, that the historical element has eclipsed the dynamic, and morphology is at a far remove from what the term indicated when it was first applied. The purpose of today’s studies is largely phylogenetic — i.e. the classification of organisms according to their genealogies — a direction initiated by Darwin’s own suggestions. The relations between the general and specific detected by these studies are taken as indicative of lines of descent, and the branching diagrams which display these relations give “evolution by descent with modification” a visible shape. The plan common to the organisms of the diagram is the plan of the common ancestor (unfortunately unknown), and commonality within transformation is understood as the common possession of static form (in practice this possession is decided on the basis of a few general characters).

    Of course, if “the theory of metamorphosis has nothing to do with this question of the historic sequence of the appearances of life,” and is “quite separate from every sort of ‛theory of descent’,” as Cassirer says, then we should expect Goethe’s notion of classification to rest on another principle, and so it does. The Type, as Goethe explained, designates potential rather than actual forms. He had considered the problem of the evolution of empirical forms, admitting that both heredity and environment would play a part in releasing or constraining the underlying potentials (Goethe, 1963: Versuch einer allgemeinen Vergleichungslehre), but he never progressed far enough to work out such an account. We can already see, however, that while the actual forms cannot be pure expression of the Type, they also could not be merely historical…

    Goethe’s Type could not be derived from anything but itself. It is thus
    a-historical. But historical influences will modify its productions…

    So IMO the diversity of life we see around us is not the result of a series of historical accidents, it is a manifestation of the general type (not to be imagined in any static historical form) expressed within the narrow confines of a material, sense experienced, organism.

  28. CharlieM: For Goethe, talk of a vital force was a needless and misleading speculation.

    How about etheric forces? Needless and misleading too?

    John Harshman:
    The point of intermediate forms is to show that transformations are plausible, though Bill claims they are not. It’s the nested hierarchy of life and its fit to the fossil record that show descent, hence transformation.

    So in the case of the butterfly leaves you agree that each leaf in the series is not a copy from the previous leaf which has been slightly altered. But in the case of sections of DNA or of proteins you do believe that this is the case. Because of their similarity you assume that one must be derived from the other by some sort of accidental duplication.

    How can you possibly read what I wrote and still interpret it that way? Once more: it isn’t just similarity that shows us phylogeny. It’s the pattern of nested hierarchy and, by the way, the fact that we can see such changes to DNA and proteins happening within populations and between generations.

    So IMO the diversity of life we see around us is not the result of a series of historical accidents, it is a manifestation of the general type (not to be imagined in any static historical form) expressed within the narrow confines of a material, sense experienced, organism.

    Isn’t “static historical form” an oxymoron? But the more important question is what this idea of the “type” explains that phylogeny does not. I see nothing there. Perhaps you could attempt to contrast the two ideas with concrete examples. When you have tried this, all your attempts have been failures.

  29. newton: I heard they fell off Noah’s Ark

    They floated. Then learned to swim. And eventually evolved into fish.

  30. Mung: They floated. Then learned to swim. And eventually evolved into fish.

    You must be confused, if that is true why are there still ducks?

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