Collective Cluelessness

No, this isn’t a post about TSZ. It’s about how to get abiogenesis without a designer and how to build a nanocar.

We have no idea how the basic set of molecules, carbohydrates, nucleic acids, lipids and proteins, were made and how they could have coupled in proper sequences, and then transformed into the ordered assemblies until there was the construction of a complex biological system, and eventually to that first cell. Nobody has any idea on how this was done when using our commonly understood mechanisms of chemical science. Those that say that they understand are generally wholly uninformed regarding chemical synthesis.

“Those that say oh this is well worked out, they know nothing, nothing, about chemical synthesis. Nothing.”

From a synthetic chemical perspective, neither I nor any of my colleagues can fathom a prebiotic molecular route to construction of a complex system. We cannot even figure out the prebiotic routes to the basic building blocks of life: carbohydrates, nucleic acids, lipids and proteins. Chemists are collectively bewildered. Hence I say that no chemist understands prebiotic synthesis of the requisite building blocks let alone their assembly into a complex system. That’s how cluelss we are.

“Nobody understand this. So if your professors say it’s all worked out, your teachers say it’s all worked out, they don’t know what they are talking about. It is not worked out.”

Given our current level of knowledge, the claim that life arose by naturalistic means must surely qualify as an extraordinary claim. A claim for which not only is there not extraordinary evidence, but a claim for which there is no objective empirical evidence whatsoever. You may as well claim to believe in magic. Sure, let’s be skeptical. You first.

265 thoughts on “Collective Cluelessness

  1. Meanwhile there is still no objective empirical evidence for the theory of abiogenesis.

    But let’s not go so far as to actually be skeptical about naturalistic OOL claims.

  2. Patrick: …it’s yet more evidence that intelligent design creationism is nothing more than a religiously motivated political movement designed to get around the separation of church and state in the U.S.

    No it isn’t.

    First, it’s just you repeating the same thing over and over. IOW, more in the sense of more of the same not more in the sense of more evidence. Second, the DI is opposed to having ID taught in public schools.

    False claims do not become true by constant repetition.

  3. Patrick: A quote mine uses excerpts to suggest that a person holds a view he or she does not, in fact, hold.

    Which is exactly why it was a quote-mine. Duh.

    SEE HERE

  4. Mung:
    Meanwhile there is still no objective empirical evidence for the theory of abiogenesis.

    True. And…?

    But let’s not go so far as to actually be skeptical about naturalistic OOL claims.

    Such as?

  5. Robin: The base theory of abiogenesis is that life arose from inert chemicals through naturalistic processes.

    Here’s what Wikipedia says:

    A scientific theory is a well-substantiated explanation of some aspect of the natural world that is acquired through the scientific method and repeatedly tested and confirmed through observation and experimentation.

    It would appear that your “theory” of abiogenesis is not a scientific theory. Do you agree that it’s not a scientific theory?

    Yet, I’d bet that if James Tour claimed that we have no scientific theory of abiogenesis people would still be outraged. Because it’s not really about the science.

  6. Mung: Here’s what Wikipedia says:

    It would appear that your “theory” of abiogenesis is not a scientific theory. Do you agree that it’s not a scientific theory?

    No, I disagree that abiogenesis is not a scientific theory since it meets the definition you provided. A number of the of the areas of research have answered questions about how chemicals come together, what chains RNA can form, how proteins develop, and so forth. All of those lines of investigation have contributed to further development of abiogenesis hypotheses, which in turn create a foundation for the theory.

    Yet, I’d bet that if James Tour claimed that we have no scientific theory of abiogenesis people would still be outraged.

    Depends on his arguments.

    Because it’s not really about the science.

    Methinks that would be your opinion based on your misunderstanding of how science actually works.

  7. Robin,

    Yet, I’d bet that if James Tour claimed that we have no scientific theory of abiogenesis people would still be outraged.

    Not particularly. But ‘t ain’t just one thing. There is promising work in abiotic synthesis of RNA bases, of sugars and amino acids, of lipids, or the formation of proton gradients which many consider a prerequisite. But there has been no – uh – synthesis as yet. Work in progress. No-one claims otherwise.

  8. The answer, though, is almost certain to be hard to find in a test tube. It happened, if it happened, in dirty water, in some unknown, probably muddy environment and the presence of unknown catalysts and cofactors. A couple of replicating molecules to start that would be very hard to detect amongst the mess that lab chemistry necessarily sweeps away.

  9. Mung:

    …it’s yet more evidence that intelligent design creationism is nothing more than a religiously motivated political movement designed to get around the separation of church and state in the U.S.

    No it isn’t.

    First, it’s just you repeating the same thing over and over. IOW, more in the sense of more of the same not more in the sense of more evidence. Second, the DI is opposed to having ID taught in public schools.

    False claims do not become true by constant repetition.

    cdesign proponentsists. You lose.

  10. Mung: Which is exactly why it was a quote-mine. Duh.

    SEE HERE

    I know you have demonstrated repeated difficulty understanding the concept “quote mine”, so I’ll type slowly this time. Nothing in the excerpt I provided suggests that Dembski holds a view other than that which the excerpt suggests he holds. The fact that he says one thing in front of non-believers and another in front of the faithful does not make what I provided a quote mine.

  11. Allan Miller,

    On what grounds do you dismiss the possibility that it is cumulative small scale evolutionary change? How would we reject this as a null hypothesis (being as how small scale evolutionary change inevitably gets bigger over broader timescales)?

    Large scale evolutionary change requires new sequences for new unique proteins either DNA sequence or splicing changes. There are approximately one million multicellular species and we cannot biochemically reconcile how any one of them originated. It is not clear to me that this is any easier then origin of life if we really understood cellular biology to the physics level. I think that supports an I don’t know as the proper scientific answer. The claims have gotten ahead of the evidence and this is going to be bad for science when the dam bursts and the general public starts to understand the controversy.

  12. Mung: Please address the post not the poster. Or are you under the impression that rule applies only to Frankie?

    I addressed both. Now please act as an adult and move on. (by the way, this post is a direct response to the contents of yours, so it is in actual fact addressing your post).

  13. Mung: I cannot believe he would be denied membership in organizations because he is willing to speak the truth.

    He speaks plenty of falsehoods (as I have clearly demonstrated) and is obviously weighed down in his thinking by an intense religious bias.

  14. Mung:
    Meanwhile there is still no objective empirical evidence for the theory of abiogenesis.

    Yes there is, your statement simply reflects your ignorance. The distribution of amino acids in the evolutionarily oldest protein domains is evidence of abiogenesis. They’re significantly saturated both in extent and relative frequency for the types of amino acids that would be predicted on thermodynamic grounds to be most easily synthesized nonbiologically.

    Now you no longer, for the rest of your life, have to repeat that basic mistake again. You are now aware of at least one piece of evidence that points to a natural origin of life. You don’t have to thank me.

  15. colewd: Large scale evolutionary change requires new sequences for new unique proteins either DNA sequence or splicing changes.

    That’s an interesting assertion. What’s your basis for making it? The general consensus of evo devo is that new proteins are seldom necessary and that slight changes in regulatory sequences can add up to big differences in development. Also, alternative splicing seems to be the case for a very small proportion of proteins.

  16. Patrick: Nothing in the excerpt I provided suggests that Dembski holds a view other than that which the excerpt suggests he holds.

    That’s why it’s a quote-mine. And by this standard, my quote of Krauss wasn’t a quote-mine either. Are you going to apologize now?

    The fact that he says one thing in front of non-believers and another in front of the faithful does not make what I provided a quote mine.

    However, it does contradict your claim that your quote of Dembski is an accurate portrayal of his views. It obviously isn’t.

    p.s. Thank you for typing slowly. Have you tried thinking slowly?

  17. John Harshman,

    That’s an interesting assertion. What’s your basis for making it? The general consensus of evo devo is that new proteins are seldom necessary and that slight changes in regulatory sequences can add up to big differences in development.

    This is a good point but eve dev changes alone don’t account for evolutionary changes. If you can cite an evolutionary transition that is accomplished with only eve devo changes that would be interesting.

  18. colewd:
    John Harshman,

    This is a good point but eve dev changes alone don’t account for evolutionary changes.If you can cite an evolutionary transition that is accomplished with only eve devo changes that would be interesting.

    So you’re free to make a claim until such time as I present a detailed example that proves you wrong? You don’t have to back that claim up with anything at all? Now that’s interesting.

    So how about the transition from chimp/human ancestor to human? How many new proteins and/or new alternative splicings? My claim would be zero and zero. There are some slightly modified proteins and a lot of regulatory changes. Don’t see anything else.

  19. colewd:
    John Harshman,
    http://www.sciencemag.org
    Science 21 December 2012:
    Vol. 338 no. 6114 pp. 1587-1593 DOI: 10.1126/science.1230612The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

    First of all, your link just goes to the Science we site, not to the article. Second, the article itself is paywalled so I can’t see what it actually says. But my guess is that they looked at mature mRNAs, not actual proteins, didn’t assay actual function, and thus might be looking at post-transcriptional noise. Is any of that correct?

  20. John Harshman,
    First, sorry the article is paywalled. Send me your email on a private message and I will send you a PDF. The article compares alternative splicing in vertebrates. I will also send you and additional paper on the subject.

  21. colewd:
    John HarshmanThe article compares alternative splicing in vertebrates.I will also send you and additional paper on the subject.

    Yes, I know it’s about alternative splicing. But that doesn’t answer either of my questions. To repeat: my guess is that they looked at mature mRNAs, not actual proteins, didn’t assay actual function, and thus might be looking at post-transcriptional noise. Is any of that correct?

  22. Mung: That’s why it’s a quote-mine.
    However, it does contradict your claim that your quote of Dembski is an accurate portrayal of his views. It obviously isn’t.

    The main problem is, Dembski is thumpingly inconsistent. Almost no matter what he says in one place, you can find another place where he says something incompatible. Some observers have speculated that this is deliberate, so that Dembski can point to something ELSE he wrote to show that his views are being misrepresented, no matter what those views might be.

    I have no idea whether this is also true of Krauss.

  23. John Harshman,

    Yes, I know it’s about alternative splicing. But that doesn’t answer either of my questions. To repeat: my guess is that they looked at mature mRNAs, not actual proteins, didn’t assay actual function, and thus might be looking at post-transcriptional noise. Is any of that correct?

    Yes, they are look at post transcriptional RNA’s.

    from the paper: A comparison of the most strongly predictive cis-elements accounting for each species’ organ- dependent splicing patterns revealed that these significantly overlap in most tissues (Fig. 3C and fig. S12). Such cis-elements may represent features comprising an ancestral vertebrate splicing code (Fig. 3D). However, the overlap between sets of splicing code features used in a given pair of species decreases with increased evolutionary distance (Fig. 3C and fig. S12; see also below). Thus, organ- dependent AS patterns appear to be generally controlled by significantly overlapping cis-regulatory codes, although progressive divergence in these codes likely also contributes to AS differences.

    Since they are seeing repeatable patterns I think this eliminates noise as a hypothesis.

  24. colewd: Since they are seeing repeatable patterns I think this eliminates noise as a hypothesis.

    Why? Tissue-specific patterns in transcription can easily represent noise. Why not patterns in splicing?

  25. John Harshman,

    Why? Tissue-specific patterns in transcription can easily represent noise. Why not patterns in splicing?

    Ok, I am interested if you still think this after reading the papers. Although it is not ultimate cause, the spliceosome and alternative splicing could be a mechanism of evolution if this data is solid.

  26. colewd:
    John Harshman,

    Ok, I am interested if you still think this after reading the papers. Although it is not ultimate cause, the spliceosome and alternative splicing could be a mechanism of evolution if this data is solid.

    Not all the way through yet, but I note the following in Irimia & Roy 2014: “Nevertheless, despite a plethora of described examples of each kind, a major unanswered question is still to what extent AS is functional or simply splicing ‘noise’” and “However, as for any modern eukaryote, it is not clear what fraction of that transcriptional diversity [in the reconstructed eukaryote common ancestor] played any relevant biological role.”

    I also note that excised exons known to produce a functional product both begin and end at codon boundaries, so that the resulting alternative isoforms are in frame. Yet a very high proportion of exons do not respect codon boundaries, suggesting that when excised they don’t produce a functional translated product.

    I don’t know a whole lot about this subject. Thanks for the reviews.

  27. colewd,

    Large scale evolutionary change requires new sequences for new unique proteins either DNA sequence or splicing changes.

    Why? You have merely declared this. How have you decided that this is what happens and not cumulative smaller-scale change and divergence?

    There are approximately one million multicellular species and we cannot biochemically reconcile how any one of them originated.

    Species originate through reproductive isolation and divergence. There is not an ‘origin’, and the mechanism is more geographic or mechanical than biochemical. Every individual is the same species as its parent. Even every step of the way from the sainted chimp-human common ancestor to the respective modern versions, or from even earlier primates, or earlier mammals … How can this be so, you might ask. I’m sure you could work it out.

    It is not clear to me that this is any easier then origin of life if we really understood cellular biology to the physics level.

    It would help, as a start, if you understood speciation.

    I think that supports an I don’t know as the proper scientific answer. The claims have gotten ahead of the evidence and this is going to be bad for science when the dam bursts and the general public starts to understand the controversy.

    If a member of the public is capable of understanding speciation, they would soon see how the ‘controversy’ is largely a result of confusion, and unwillingness or incapacity to adopt the evolutionary stance even for the purposes of argument. Among the evolution-blind, conversely, it’s a lost cause. Bring on the next straw man.

  28. colewd,

    If you can cite an evolutionary transition that is accomplished with only eve devo changes that would be interesting.

    It’s one or the other is it? Change in gene products or changes in regulation. Heh heh. Regulation involves gene products, y’know.

    Still, what would you suggest was involved in the divergence of the Spotted and Common Sandpiper? Many novel proteins? How about the sandpipers and the stints? Was that a bigger change (when it happened)?

    colewd,

    from the paper: […] However, the overlap between sets of splicing code features used in a given pair of species decreases with increased evolutionary distance (Fig. 3C and fig. S12; see also below). Thus, organ- dependent AS patterns appear to be generally controlled by significantly overlapping cis-regulatory codes, although progressive divergence in these codes likely also contributes to AS differences.

    Divergence in splice codes is expected to follow divergence in everything else. It’s entirely in accord with the gradualist evolutionary paradigm. Splicing is after all under genetic control. So what, other than contrarianism, would lead you to elevate this beyond the rest of genetics to a primary causal role? You seem happy to summarily dismiss the entirety of current knowledge but eagerly lasso any passing cloud.

  29. Mung:

    Nothing in the excerpt I provided suggests that Dembski holds a view other than that which the excerpt suggests he holds.

    That’s why it’s a quote-mine. And by this standard, my quote of Krauss wasn’t a quote-mine either. Are you going to apologize now?

    No, a quote mine is when one takes an excerpt out of context and uses it to suggest that the person being quoted holds a position other than what he or she actually holds. Dembski actually said “Intelligent design is just the Logos theology of John’s Gospel restated in the idiom of information theory.” and he meant it.

    You, on the other hand, wrote this:

    “Evolution is a directed process…it’s directed.”

    – Lawrence Krauss

    Lawrence Krauss must be an IDiot.

    You removed significant context and suggested that Krauss holds a view that he, in fact, opposes.

    The fact that he says one thing in front of non-believers and another in front of the faithful does not make what I provided a quote mine.

    However, it does contradict your claim that your quote of Dembski is an accurate portrayal of his views. It obviously isn’t.

    It absolutely is. Read the Touchstone article.

    p.s. Thank you for typing slowly. Have you tried thinking slowly?

    No, I leave that to the intelligent design creationists.

  30. Science is about social momentum. It’s a circus of controversy, particularly origin of life science, which isn’t really even a science — it’s a Big Top of exquisite conjecture, a field of wild imaginings waiting to be tamed inside the Who We Are And Where We Came From tent. No one can yet say what the origin of life narrative is despite the fanfare: trumpets, thundering hooves, flared nostrils, firebreathing and other posturing, and so the clash of “expert” opinion makes for a light show with all the color of a supercollider collision event. . .

    – Susan Mazur

  31. What Freeman Dyson, Institute for Advanced Study emeritus professor (Chapter 8), told Charlie Rose over the PBS roundtable several years ago still holds: “we are all equally ignorant” when it comes to origin of life. Or as synthetic biologist Steve Benner (Chapters 4, 6) puts it, “there are no experts.”

    Mazur, Suzan. The Origin of Life Circus: A How To Make Life Extravaganza

  32. …I must say I was very much underwhelmed by the breadth of their proposals. Even the experts I drew together in San Diego a month or so ago, even they don’t have a single clear model of how life began. There’s no universal agreement. We don’t have a theory. We’re a long way from home base. Probably 10 or 20 years away before we have a plausible model and even further out into the future before we can say we know how life began. I’ll be dead before people can make that statement.

    – Harry Lonsdale

  33. Rumraket,

    But nobody here is disputing that we don’t know how life began. So what?

    That leaves a big gap for Mung’s God to scurry into. Right, Mung?

  34. Yep. ‘We don’t know’ trades for ‘But we know, don’t we kids wink wink’.

  35. Mung,

    Mazur: “No one can yet say what the origin of life narrative is despite the fanfare: trumpets, thundering hooves, flared nostrils, firebreathing and other posturing, and so the clash of “expert” opinion makes for a light show with all the color of a supercollider collision event. . .”

    Never knowingly undersold.

  36. From that interview:

    Suzan Mazur: Chris McKay once told me the following: “The Darwinian paradigm breaks down in two obvious ways. First, and most clear, Darwinian selection cannot be responsible for the origin of life. Secondly, there is some thought that Darwinian selection cannot fully explain the rise of complexity at the molecular level. . . . It can’t be Darwinian all the way down. . . . Darwinian selection only works when there’s software. And everything that’s prebiotic is hardware.” Again, “life” has been defined on the Origin of Life Challenge website as “a self-sustaining chemical system capable of undergoing Darwinian evolution.” My question is that by steering your prizewinning search for the origin of life in the direction of Darwinian science, which is now being seriously marginalized in light of the “evo-devo revolution” — as Noam Chomsky put it — and the evolution paradigm shift, with some of our most esteemed scientists declaring neo-Darwinism dead — the accumulation of genetic mutations being enough to change one species to another having not been validated in the literature — are you concerned that you and your panel may have angled the prize in the direction of false hypotheses?

    What the flying fuck is she babbling about?

  37. Mung: No one can yet say what the origin of life narrative is despite the fanfare: trumpets, thundering hooves, flared nostrils, firebreathing and other posturing. . .

    Could some one here (Mung?) perhaps point me to some of all this bluster and bravado Mazur refers to? I haven’t seen it myself.

  38. keiths: That leaves a big gap for Mung’s God to scurry into. Right, Mung?

    Another person who didn’t watch the video. Right keiths?

  39. Rumraket: But nobody here is disputing that we don’t know how life began. So what?

    We’re ignorant. We don’t know. Great! And we don’t accept claims without objective empirical evidence. And no one here actually believes in a naturalistic origin of life.

  40. Mung,

    And no one here actually believes in a naturalistic origin of life.

    Finally, something to agree on. ‘Believing in’ things is not required.

  41. Mung: We’re ignorant. We don’t know. Great! And we don’t accept claims without objective empirical evidence. And no one here actually believes in a naturalistic origin of life.

    Those are two separate (but related) questions. Is there evidence for a natural origin of life? (Yes there is, I already mentioned some) and do we know in detail how it happened? (No we don’t).

  42. Mung: We’re ignorant. We don’t know. Great! And we don’t accept claims without objective empirical evidence. And no one here actually believes in a naturalistic origin of life.

    Why would we?

    On the other hand, we do believe that known causes are justified in hypotheses, while unknown causes are not. Hence we’re not chasing down every speculative claim and considering its “possibility” for making life in the first place, but consider known causes when hypothesizing how life arose.

    We don’t believe in just making it all up.

    Glen Davidson

  43. Suzan Mazur: Who is your origins professor?

    Lawrence Krauss: Rob Boyd, an evolutionary psychologist and anthropologist from UCLA.

    *snicker*

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