The Skeptics Wink and Nod.

Here is an informative little video by a guy named Steve Mould who does a lot of “science” videos on youtube.  Its all (ostensibly) about how simple little processes can make “meaningful” structures from stochastic processes-and he uses magnetic shaped little parts to show this.  Its a popular channeled followed by millions, and is often referenced by other famous people in the science community-and his fans love it.

And hey, it does show how meaningful structures CAN form from random processes.  Right?  So you can learn from this.  Wink, wink.  Nod, nod. And all the skeptics will know exactly what he is really saying.  Cause we are all part of the clique that knows this language-the language of the skeptic propagandist.  I mean, he almost hides it, the real message, it is just under the surface, and the less skeptically aware, the casualist, might even miss it.  The casualist might not learn as much about Steve Mould and what he is trying to say here-but the skeptic knows.  “See, atheism is true! Spread the word!” Steve has given the wink. The same wink used by DeGrasse Tyson, and Sean Carroll, Lawrence Krauss, Brian Greene, and on and on.  You know the one.

And for 95% of his viewers, whether they know it or not, they got his message.  I mean, look, its plain as day, right?  He just showed you, that is certainly a meaningful structure that arose from random processes, isn’t it?  Its defintely meaningful, its a, a, a , well, it’s shape that, we have a, a  name for…that’s kind of…anyway, defintely random, I mean other than the magnets and the precut shapes, and the little ball with nothing else inside, and the shaking only until its just right then stopping kind of way…That’s random kind of right???

But there are 5% percent of his viewers that spotted his little wink and nod, and said, hold on a second.  If you want us to believe that your little explanation about how simply life can form from nonsense without a plan, how blind exactly do you want us to be?  95%, they are hooked, you got them (Ryan StallardThere are so many creationist videos this obliterates. Especially 4:18.). But some likeGhryst VanGhod helpfully point out: “this is incorrect. the kinesin travels along fibres within the cell and takes the various molecules exactly where they need to be, they are not randomly “jumbling around in solution”. https://youtu.be/gbycQf1TbM0  ” and then you get to see a video that tells you just a few more of the things that are ACTUALLY happening which are even more amazing if you weren’t already skeptical (the real kind).

And if you go through some more of the comments you will notice a few more (real) skeptics, not the wink and nod kind, and you will start to notice why the wink nod propogandist skeptics everywhere you look in modern culture are a very puposefully designed cancer on knowledge and thought.

1,212 thoughts on “The Skeptics Wink and Nod.

  1. OMagain: I’d like to understand how phoodoo goes from his particular set of beliefs in a particular set of god(s) to advocating putting people in concentration camps. That might clarify things a little.

    Didn’t he say only people that deserve it?

    Though the criteria on which one decides who qualifies for internment and re-education with forced labour and who doesn’t can be added to the list of questions phoodoo hasn’t addressed.

  2. Corneel: Words do not dictate reality or our ideas about them, so I don’t understand why you do not just accept that other people understand the term differently. That might help the discussion.

    Paraphrasing Ghandi’s answer when asked what he thought of British civilization:

    I think discussion with phoodoo would be a very good thing.

  3. I can’t look away from the gentle train wreck that is Uncommon Descent these days. William J. Murray (I mentioned him earlier) has been promoting his latest worldview (MRT where the T stands for theory – but that’s not important right now) and making similar points on sock-gnome arguments. Here’s an example but the whole thread is quite amusing (I may have odd tastes).

  4. Alan can’t stop talking about design without wanting to know what the God is like.

    Not wanting to believe something is a powerful motivator.

  5. DNA_Jock: …(CharlieM’s) Science Daily blurb from Urbana-Champaign refers to “high energy bonds”, which makes me scream.

    Is this some sort of sexual thing? Nudge, nudge, 😉 😉 🙂

    Getting back to the serious discussion, can you clarify this?

  6. phoodoo: Alan can’t stop talking about design without wanting to know what the God is like.

    ‘The’ god? It got a name, this god of yours?

    We know what your god is like. It’s like you. That’s why it’s your god. You see yourself reflected in what you imagine it to be.

  7. phoodoo: Not wanting to believe something is a powerful motivator.

    But that’s your imagination. Nobody thinks like that, except you I suspect.

    You know the evidence is not on your side. You don’t want to believe evolution is a good explanation for some aspects of life. So you don’t.

    How do explain the many scientists working in the field of evolution who are themselves theists?

    What is their motivation? They believe in god and science. There are no conflicts there. There is no cross over. There is no problem.

    But you for some reason think that your god and evolution are incompatible. How sad. What a paucity of imagination you must have.

  8. phoodoo: Not wanting to believe something is a powerful motivator.

    You believe dogs use PSI to detect when their owners are on the way home.

    Wanting to believe something is an even more powerful motivator it seems.

  9. CharlieM: Getting back to the serious discussion, can you clarify this?

    Sure. A lot of people (mainly science writers, but some of them biochemists, I’m afraid) talk of the “high energy bond” in ATP. That pyrophosphate bond is important because it is, in fact, a low energy bond, and therefore breaking it and forming other bonds is favorable. Anyone who knows a bit of chemistry is going to note that it is the hydrolysis of that bond that produces energy, and avoid referring to pyrophospate as a “high energy bond”; Metzler, for example, refers to it as having “high group transfer potential”.

  10. phoodoo: The word comes from telos-which literally means an ultimate object or aim, a goal.The plan is to achieve that goal.

    So now you want to use the word to mean trying to achieve a target or goal without planning to reach a target or goal?

    I think there’s a mistake here between teleology and intentionality — concepts that are, to be sure, closely related!

    Teleology can be thought of as “having a purpose” or more liberally as “being organized in purposive ways”. Chemotaxis in bacteria, mentioned above, is a kind of teleology because the bacteria has a goal, and its behavior makes sense in light the goal it is trying to achieve.

    This doesn’t require that the bacteria understand what its goal is, or even have a mental representation of that goal. (There’s a lively debate about whether intentionality always requires representations. I won’t get into that right now.)

    So, even though the bacterium itself cannot form a representation of the state it aims to bring about and then organize it behavior in order to bring about that state, its behavior is still goal-oriented.

    Alan Fox:
    I can’t look away from the gentle train wreck that is Uncommon Descent these days. William J. Murray (I mentioned him earlier) has been promoting his latest worldview (MRT where the T stands for theory – but that’s not important right now) and making similar points on sock-gnome arguments. Here’s an example but the whole thread is quite amusing (I may have odd tastes).

    What I find fascinating and hilarious is that no one at Uncommon Descent knows enough philosophy to explain to Murray the exact nature of the mistake he’s making. It’s just one big circular firing squad over there.

  11. On two random sources that discuses teleology the word “plan” is literally not on the page.

    The word comes from telos-which literally means an ultimate object or aim, a goal.The plan is to achieve that goal.

    So now you want to use the word to mean trying to achieve a target or goal without planning to reach a target or goal?

    No, the bit about “the plan is to achieve that goal” and the rest of it – you added that phoodoo.

    You took the words meaning as defined, decided that it was insufficient and are now berating everyone for not using the word in the way you have adjusted it.

    So very sad.

  12. phoodoo,
    Is this what you are calling the modern synthesis? That living cells are machines that construct their own parts?

    Thanks for confirming that you don’t know what the modern synthesis is. It’s obvious from your mistaking evolution for “random nothingness created everything” though. So, there was no need for confirmation.

    phoodoo,
    Do you believe physics alone can not explain where we came from?

    Depends on how physics is defined. By most common definitions, physics tends to be too reductionistic to get us there. We need several levels of analysis to start understanding how things work. However, some define complexity theory and other “building up” efforts as physics too. But I don’t know if that will be enough. I think, however, that we have very good foundations. At least enough for anyone who actually cares about having some basic understanding.

    phoodoo,
    The modern synthesis is founded in morphogenetic fields? Are you a closet Rupert Sheldrake fan?

    Are you mistaking whatever you quoted for something I said? Are you mistaking whatever you quoted for the modern synthesis? You are spectacularly lost.

  13. Entropy: Are you mistaking whatever you quoted for something I said? Are you mistaking whatever you quoted for the modern synthesis? You are spectacularly lost.

    I decided to dig a little deeper into phoodoo’s quote that included that slightly strange usage of “morphogenetic field” (but did use quotation marks in the original, as if to convey “so-called”). The quoted text appeared to be ascribed to Goodwin, in that phoodoo ended the blockquote thus

    …a creative power that forces it all. – Goodwin

    but no, the quoted text is in fact authored by a somewhat eccentric Swedish literary academic: his amazon book review of Nature’s Due ends

    creative power that forces it all. – Goodwin was the head of a oneyear-course in Holistic Science for MSc at Schumacher College in Devon in England. Tragically he died on July 15th 2009, 78 years old.

    phoodoo clipped the bit he didn’t want.
    Soooo
    Goodwin –> Lagerroth’s amazon book review –> “morphogenetic field” (a commonplace term in conventional developmental biology) –> morphic resonance (Sheldrake’s woo).
    Therefore if you cite Goodwin, you must be a closet Sheldrake fan.
    Do try to keep up… <ggg>

  14. Kantian Naturalist: I think there’s a mistake here between teleology and intentionality — concepts that are, to be sure, closely related!

    Teleology can be thought of as “having a purpose” or more liberally as “being organized in purposive ways”.Chemotaxis in bacteria, mentioned above, is a kind of teleology because the bacteria has a goal, and its behavior makes sense in light the goal it is trying to achieve.

    This doesn’t require that the bacteria understand what its goal is, or even have a mental representation of that goal.(There’s a lively debate about whether intentionality always requires representations. I won’t get into that right now.)

    So, even though the bacterium itself cannot form a representation of the state it aims to bring about and then organize it behavior in order to bring about that state, its behavior is still goal-oriented.

    What I find fascinating and hilarious is that no one at Uncommon Descent knows enough philosophy to explain to Murray the exact nature of the mistake he’s making. It’s just one big circular firing squad over there.

    I don’t know what having a purpose means to you. Songs have a purpose. Breathing has a purpose. I have no idea what that has to do with teleology.

    It’s not practical to wade through your new definitions of words. Teleology already has a meaning, and I have no reason to believe that all these authors you referenced have decided to give the word a new meaning only they know.

    Regardless, is your idea of teleology in life a scientific one or a philosophical one? Because, this is your complaint about intelligent design, that it’s not science. How is what you are saying more science than intelligent design.
    As far I I am concerned, if it’s investigating what is true, that that is science.

  15. phoodoo: As far I I am concerned, if it’s investigating what is true, that that is science.

    Well, apart from perhaps quibbling over “true” and suggesting “most accurate explanation” instead, I agree. Using a scientific approach involves making observations and conducting experiments to obtain data that may or may not support hypotheses proposed as explanations for observed phenomena.

    How does the “Intelligent Design” approach differ?

  16. Kantian Naturalist: Chemotaxis in bacteria, mentioned above, is a kind of teleology because the bacteria has a goal, and its behavior makes sense in light the goal it is trying to achieve.

    How do you determine what the goal of the chemotaxing bacterium is? Converting ATP into movement? Stirring the surrounding medium? Keeping macrophages busy? Behave in a way that is more likely to pass on it’s genes to the next generation? Causing phoodoo’s head to explode again? Us having this discussion?

    Again I think what we can say is really just that we can describe the bacterium has having a goal(or several). It is a framing we can put on certain processes or histories of events, but we have to decide the context and what we consider the goal pretty much arbitrarily. I don’t think the bacterium really “has” a goal, as if we could somehow take it apart and find the goal-atoms inside it.
    The bacterium has attributes and constituents, and these define and cause it’s behavior. But we are the ones imagining a goal for it. We are the ones framing some particular behavior as being goal-oriented. The goal exists only in our own minds, it is not a part or attribute of the bacterium itself. History will continue for the bacterium and it’s constituents long after it reaches whatever “goal” we imagine in our own minds that it has.

    What I think is most important here is that while we can describe any sort of change that occurs (whether the behavior of living organisms, or just atmospheric or geological processs) in the framing of teleological language, it is possible to describe anything the bacterium does without reference to any goals, merely as mechanistic processes, and we can explain the origin and persistence of it’s behaviors as products of those same processes.

    There is nothing about the bacterium’s behavior that demands or compels a teleological description, and ultimately it seems to me to add nothing in the way of helping us understand what is really going on “under the hood” so to speak.

    The biochemical and physical basis for chemotaxis was not alighted upon by considering the bacterium as having goals, but by considering it as a system of interacting atoms and molecules. That is what allowed us to understand how chemotaxis works.

  17. Rumraket: There is nothing about the bacterium’s behavior that demands or compels a teleological description, and ultimately it seems to me to add nothing in the way of helping us understand what is really going on “under the hood” so to speak.

    Yet you often talk about the function of proteins. How can a protein have a function but no purpose?

    Although I agree with most of what you wrote, I disagree that no understanding is gained by using teleological language. In fact, I could easily point to half a dozen instances where you yourself use teleological language to aid understanding, like in the example above.

    So while I agree that non-conscious biological processes can be described in purely mechanistic terms and acknowledge that teleological language confuses people of a certain bent, I disagree that the subjects we describe in teleological language are chosen arbitrarily or that such language lacks educational merit.

  18. Corneel: Yet you often talk about the function of proteins. How can a protein have a function but no purpose?

    I’m not saying proteins can’t have a purpose(only that it’s not an attribute of the protein itself). What I’m saying is that the purpose exists only as an idea in your head when you think about the protein and try to characterize what it does. But you can declare any attribute or effect of the protein’s existence to be it’s purpose, and yes I would say that is what I am doing when I describe a particular protein as having a particular function.

    I am arbitrarily picking some effect it has in the real world and saying, in effect, that this is what it is for. I just admit, I recognize, that this is what I am doing. I could say the protein’s function is to weigh X number of daltons, or to serve as a sink for carbon, oxygen, and nitrogen. Or to take up the space it occupies. Those are among the real effects it has. I could pick any of the effects or attributes of the protein and call that it’s purpose, or it’s function. That it exists to do that, or be that. And who are you or anyone else to tell me that I am wrong, and that it’s real/true/objective/correct function/purpose/end/goal is some other effect or attribute? Why is it more true to say it’s function is to do X, than it is to do Y?

    Corneel: Although I agree with most of what you wrote, I disagree that no understanding is gained by using teleological language. In fact, I could easily point to half a dozen instances where you yourself use teleological language to aid understanding, like in the example above.

    What example?

    Corneel: I disagree that the subjects we describe in teleological language are chosen arbitrarily

    I don’t see how you could possibly disagree with that. What is it based on that isn’t ultimately an arbitrary imposition on whatever effects it might have?

    Corneel:
    or that such language lacks educational merit.

    Well I can only say that I haven’t seen any good evidence that teleological language actually furthers understanding on subjects of evolution, physics, or biochemistry. Are there any studies where they try to directly compare teaching approaches where they teach students to understand some physical or chemical process, using teleological vs non-teleological language?

  19. DNA_Jock:
    CharlieM: Getting back to the serious discussion, can you clarify this?

    DNA_Jock: Sure. A lot of people (mainly science writers, but some of them biochemists, I’m afraid) talk of the “high energy bond” in ATP. That pyrophosphate bond is important because it is, in fact, a low energy bond, and therefore breaking it and forming other bonds is favorable. Anyone who knows a bit of chemistry is going to note that it is the hydrolysis of that bond that produces energy, and avoid referring to pyrophospate as a “high energy bond”; Metzler, for example, refers to it as having “high group transfer potential”.

    You have confused me, so I’ve looked at the translation process in more detail. Now I suspect you may have also confused yourself.

    Here again is the paragraph you have an issue with:

    Synthetases charge the amino acids with high-energy chemical bonds that speed the later formation of new peptide (protein) bonds. Synthetases also have powerful editing capabilities; if the wrong amino acid is added to a tRNA, the enzyme quickly dissolves the bond.

    Obviously they are not talking about the ATP bonds as these are long gone by the time elongation takes place and so cannot be the bonds under discussion.

    So where does the ATP fit into the translation process? Initially ATP is added to the free amino acid releasing pyrophosphate to produce AMP. The aminoacyl-tRNA synthetase enzyme takes this molecule and attaches it to the correct tRNA which releases the AMP. Now the amino acid is bonded to the tRNA ready to be introduced to the ribosome. They are talking about the energy contained in the amino acid-tRNA bond.

    Now I read the the following from Columbia University:

    The energy derived from splitting the tRNA-AA (really the tRNA-chain) bond drives peptide bond synthesis. In other words, the AA~tRNA connection is a high energy bond. How it is formed at the expense of ATP is discussed below.

    So what reason do I have for believing you rather than them?

  20. Looking at translation processes in protein synthesis, the explanation that free floating amino acids just happen to bump into tRNAs which happen to bump into ribosomes becomes so simplified that it is a non-explanation. And we should not forget that all the players in this process must be present and available in the suitable quantities at the right time and place. The factors that ensure this is the case range from the organism finding enough of the correct food down to the cells being able to transfer materials to and from the circulatory system whether that system is integral or external to the organism.

    In reality there are a host of enzymes ensuring that amino acids are correctly attached to their corresponding tRNAs which are then associated with a newly assembled ribosome and undergo the three stage process of forming the peptide chain. There are some excellent videos showing these processes, this one among them. It gives an easy to follow explanation of the translation processes from start to finish.

    This process is fundamental and vital for living systems and no living cell could exist without it.

  21. CharlieM: So what reason do I have for believing you rather than them?

    Because I am right and they are wrong.
    Not very helpful, no? The idea that you can resolve these questions by an appeal to competing authorities is, frankly, bizarre.
    Read Metzler. It’s available on Amazon, but be aware that it comes in two volumes these days: you need the first volume.
    Or you could read up online about what bond energy is, and (and this is the important step) think about it.

    The larger the average bond energy, per electron-pair bond, of a molecule, the more stable and lower-energy the molecule.

    I have not confused myself: I am familiar with the mechanism of charging enzymes.
    ETA for clarity: like the pyrophosphate bond, the aa~tRNA connection is a low energy bond, a “high group transfer potential” often mislabeled as a “high energy bond”.

  22. CharlieM: So what reason do I have for believing you rather than them?

    This depends in this case on your own knowledge of biochemistry. If you learned about chemical thermodynamics, exothermic and endothermic reactions, I’m sure you’d be able to follow the reasoning. Was your formal education in the UK? Did you take GCEs at “O”and “A” level in the sciences, physics, chemistry, biology? Degree course in a related subject? Without some knowledge and experience in the field it is not easy to make informed judgements directly about ofhers’ competence. Mind you these days, internet resources enable us to inform ourselves on matters of interest much more easily, needing only time and a terminal.

  23. CharlieM: Looking at translation processes in protein synthesis, the explanation that free floating amino acids just happen to bump into tRNAs which happen to bump into ribosomes becomes so simplified that it is a non-explanation

    No, it doesn’t. That’s false. That free amino acids encounter tRNA-synthetases, which encounter tRNA, which encounters ribosomes really does constitute a part of the explanation for the things that occur during coded protein biosynthesis.

    It just doesn’t constitute an explanation for everything that occurs inside the cell. Yes, this process is itself a part of other processes on which it relies. And yet these particular events are still stochastic elements of the process of translation.

    CharlieM:
    And we should not forget that all the players in this process must be present and available in the suitable quantities at the right time and place.

    Nobody forgets that.

    CharlieM: This process is fundamental and vital for living systems and no living cell could exist without it.

    That depends on what you define to be a living cell, doesn’t it?

    How about a mixed amphiphile+fatty acid bilayer vesicle powered by a local geologically hosted metabolism, encapsulating a set of collectively replicating ribozymes, yet without coded protein biosynthesis, being based in part on very short but continuously generated set of random-sequence peptides performing rudimentary functions? – That would fail to qualify for your definition of a “living cell” or “living system”(?) because you seem to have merely said that by definition a living cell/system must have coded protein biosynthesis.

    But a system such as the one I described is a candidate stage in the evolution of living cells as we know them. What use is it to declare that such a system is not a form of life, if there really was such a stage in life’s eventual emergence?

  24. DNA_Jock:
    CharlieM: So what reason do I have for believing you rather than them?

    DNA_Jock: Because I am right and they are wrong.
    Not very helpful, no? The idea that you can resolve these questions by an appeal to competing authorities is, frankly, bizarre.
    Read Metzler. It’s available on Amazon, but be aware that it comes in two volumes these days: you need the first volume.
    Or you could read up online about what bond energy is, and (and this is the important step) think about it.

    “The larger the average bond energy, per electron-pair bond, of a molecule, the more stable and lower-energy the molecule.”

    I have not confused myself: I am familiar with the mechanism of charging enzymes.
    ETA for clarity: like the pyrophosphate bond, the aa~tRNA connection is a low energy bond, a “high group transfer potential” often mislabeled as a “high energy bond”.

    I’m not appealing to anyone, I’m trying to make sense of this divergence of positions. If so many scientists are getting this wrong maybe they should be encouraged to be more specific about what they mean by “high energy”.

    You may not be confused about bond energies but it seemed to me you were confused about which specific bonds they were discussing. I was confused about the role of ATP in translation and from what you said I thought it must be directly involved in the process of peptide formation within the ribosome. Out of interest do you know of any high energy bond manipulation involved in translation?

    But all this is distracting from understanding the actual processes involved in protein synthesis. In my opinion adding enzymes piecemeal to a much simpler system just would not work.

  25. Alan Fox:
    CharlieM: So what reason do I have for believing you rather than them?

    Alan Fox: This depends in this case on your own knowledge of biochemistry. If you learned about chemical thermodynamics, exothermic and endothermic reactions, I’m sure you’d be able to follow the reasoning. Was your formal education in the UK? Did you take GCEs at “O”and “A” level in the sciences, physics, chemistry, biology? Degree course in a related subject? Without some knowledge and experience in the field it is not easy to make informed judgements directly about ofhers’ competence. Mind you these days, internet resources enable us to inform ourselves on matters of interest much more easily, needing only time and a terminal.

    I do have a few “O” grades and “Highers” which are the Scottish version of “O” and “A” levels. Included among these is a “higher” in human biology. Other than this my qualifications are few and far between. I’ve never been interested in amassing bits of paper.

    I don’t think it is unreasonable for me to ask DNA_Jock to clarify why he had such an emotional response to that statement by the University of Illinois at Urbana-Champaign, and why he specified ATP bonds in his argument.

    Either way I now know much more about the processes of translation than I did before this discussion.

  26. Alan Fox:
    CharlieM: So what reason do I have for believing you rather than them?

    Alan Fox: This depends in this case on your own knowledge of biochemistry. If you learned about chemical thermodynamics, exothermic and endothermic reactions, I’m sure you’d be able to follow the reasoning. Was your formal education in the UK? Did you take GCEs at “O”and “A” level in the sciences, physics, chemistry, biology? Degree course in a related subject? Without some knowledge and experience in the field it is not easy to make informed judgements directly about ofhers’ competence. Mind you these days, internet resources enable us to inform ourselves on matters of interest much more easily, needing only time and a terminal.

    I do have a few “O” grades and “Highers” which are the Scottish version of “O” and “A” levels. Included among these is a “higher” in human biology. Other than this my qualifications are few and far between. I’ve never been interested in amassing bits of paper.

    I don’t think it is unreasonable for me to ask DNA_Jock to clarify why he had such an emotional response to that statement by the University of Illinois at Urbana-Champaign, and why he specified ATP bonds in his argument.

    Either way I now know much more about the processes of translation than I did before this discussion.

  27. CharlieM:But all this is distracting from understanding the actual processes involved in protein synthesis.

    There’s always the possibility to start another thread. But ATP is central to protein synthesis providing the necessary energy.

    In my opinion adding enzymes piecemeal to a much simpler system just would not work.

    Is that just a gut feeling or can you suggest why incremental changes would not work?

  28. CharlieM: I do have a few “O” grades and “Highers” which are the Scottish version of “O” and “A” levels. Included among these is a “higher” in human biology. Other than this my qualifications are few and far between. I’ve never been interested in amassing bits of paper.

    They get lost anyway.

    I don’t think it is unreasonable for me to ask DNA_Jock to clarify why he had such an emotional response to that statement by the University of Illinois at Urbana-Champaign, and why he specified ATP bonds in his argument.

    Press releases often oversell university studies to the extent of misrepresenting them.

    Either way I now know much more about the processes of translation than I did before this discussion.

    Well, that’s a result.

  29. CharlieM: In my opinion adding enzymes piecemeal to a much simpler system just would not work.

    What worth should we attach to your opinion? The vast majority of the people most qualified on the question of the origin of the translation system don’t seem to agree with you, and it gets worse for you once we consider the fact that we have evidence that the translation system, at least, used to be simpler than the one we have now, and that considerably fewer amino acids were encoded in the genetic code.

    Heck, even the ribosome itself shows evidence of it’s own evolution, and that it ultimately derives from a single, duplicated RNA sequence that can catalyze peptide bond formation when it dimerizes. This was long speculated, and finally tested this year:
    Xu D, Wang Y. Protein-free ribosomal RNA scaffolds can assemble poly-lysine oligos from charged tRNA fragments. Biochem Biophys Res Commun. 2021;544:81-85. doi:10.1016/j.bbrc.2021.01.036 https://pubmed.ncbi.nlm.nih.gov/33545497/

  30. CharlieM: Obviously they are not talking about the ATP bonds as these are long gone by the time elongation takes place and so cannot be the bonds under discussion.

    Actually, this is wrong too — the result of Charlie’s belief that it is not all random jostling. News flash Charlie: these reactions can potentially run in reverse.
    Charlie’s Columbia source notes [here’s a link to it that works]

    In other words, the AA~tRNA connection is a high energy bond. How it is formed at the expense of ATP is discussed below.

    If Charlie had kept reading, he would have got to the discussion below, viz:

    (rxn 1) tRNA + AA → AA~tRNA (+ water )
    (rxn 2) ATP (+ water) → AMP + PPi
    (rxn 3) Pyrophosphatase: PPi (+ water) → 2 Pi
    Rxn1 is uphill, so you must couple rxn (1) to hydrolysis of ATP (rxn 2).
    Net result of (1) + (2) = ATP + AA + tRNA → AMP + PPi + AA~tRNA
    Net result of (1) + (2) + (3) = ATP + AA + tRNA (+water) → AMP + 2Pi + AA~tRNA
    Δ Go for (1) + (2) is about zero, but PP ‘tase = pyrophosphatase removes product (rxn. 3) and pulls the overall reaction to the right (as in nucleic acid synth.). In other words, sum of Δ Go for (1) + (2) + (3) is negative. Now the AA~tRNA can be used in protein synthesis to provide free energy for formation of peptide bonds.

    TLDR version: the cleaving of that “long gone” pyrophosphate by water is what actually drives peptide synthesis forwards. It is entirely necessary part of the process because otherwise, the reaction could reverse itself.
    My complaint is with the use of the term ‘high energy bond’ to describe a bond whose cleavage is energetically favorable, those are low energy bonds; phosphate anhydride is merely the most famous example; aa~tRNA is the third most famous, after PEP.
    They have “high group transfer potential” .

  31. Corneel,

    You can not talk about biology in any detail at all, without using teleological language. Rummy can’t do it, no one can do it, because it just sounds too ridiculously unbelievable. The question is one of differentiating between what is reasonable to call accidents vs on purpose. Of course the evolutionists hate the use of the word accident, but that is what we use in English to mean not on purpose, not with intent.

    So once KN or others start trying to use the word purpose to talk about biology, they have to mean its not an accident. In other words it was planned.

    Unfortunately, KN is now trying to make the use of all of these words so convoluted as to remove any meaning from them at all. But to most people the meaning of teleology is clear. And that meaning is the opposite of a happenstance accident, and rather means it happened by design. It was intending to reach a point further along in time, a goal.

    Now I ca see why someone like Rummy will start doing all kinds of jumping in the air and waving his hands saying “nothing is teleological” because he also knows what the word means and implies. Others who also know what the word really means, prefer to just try to distort what it means beyond recognition, because if they used the word as it is intended, again, its a plan, and a design.

    But the authors of the books KN cited all used the word teleology. Its ridiculous to assume they all are using a meaning that is contrary to the conventional meaning.

  32. DNA_Jock: creative power that forces it all. – Goodwin was the head of a oneyear-course in Holistic Science for MSc at Schumacher College in Devon in England. Tragically he died on July 15th 2009, 78 years old.

    I love this ridiculous conspiracy theory of yours-that I was afraid to mention that Goodwin was the head of something that is called Holistic Science. Or that tragically he is dead? What Jock??

    Don’t worry , I will have plenty of more time to ridicule the idiotic post you made saying morphogentic fields have nothing to do with Sheldrakes ideas-as if I was confusing the two-when its you who was confused. Now you are trying some diversion tactic.

    Why would I care if people knew Goodwin believed in holistic science? Its sort of the point-which you once again!, don’t get. I guess you need more math symbols to keep you from being confused.

  33. phoodoo: The question is one of differentiating between what is reasonable to call accidents vs on purpose.Of course the evolutionists hate the use of the word accident, but that is what we use in English to mean not on purpose, not with intent.

    I suspect terminology is not our friend in this discussion. Consider the phenomenon of water running downhill. Does water intend to run downhill? I doubt if water has any intentions. So does water run downhill by accident? Well, I would venture that gravity plays a role.

    But wait! Does gravity intend for water to run downhill? I’d have trouble constructing a reasonable phrase to describe gravity having wants, desires, or purposes. But things aren’t attracted by gravity by accident either.

    Surely you yourself could come up with many such examples, of clearly mindless forces or processes nonetheless producing predictable, non-accidental results. Water does not run downhill either on purpose or by accident. Your dichotomy is flawed.

  34. phoodoo: I love this ridiculous conspiracy theory of yours-that I was afraid to mention that Goodwin was the head of something that is called Holistic Science. Or that tragically he is dead? What Jock??

    Heavens, no! I merely noted that you clipped the bit you didn’t want. No motivation was suggested. I am happy to accept your stipulation that you DID want the clipped text, but were unsuccessful in your efforts to copy and paste. You seem a little touchy.

    Don’t worry , I will have plenty of more time to ridicule the idiotic post you made saying morphogentic fields have nothing to do with Sheldrakes ideas-as if I was confusing the two-when its you who was confused. Now you are trying some diversion tactic.

    Not my argument; obviously, Sheldrake’s goofy ideas, such as Morphic Resonance, seek to explain how morphogenetic fields work. But “morphogenetic fields” is a commonplace term in conventional, non-woomeister developmental biology, so your claim that the use of the phrase somehow references Sheldrake’s ridiculous woo is erroneous. You wrote:

    The modern synthesis is founded in morphogenetic fields? Are you a closet Rupert Sheldrake fan?

    Let’s not get diverted; I look forward to the copious ridicule that you have plenty of time to heap upon me. Perhaps you will even explain why Jaytee went to the window before Pamela started home.

  35. Flint: I suspect terminology is not our friend in this discussion. Consider the phenomenon of water running downhill. Does water intend to run downhill? I doubt if water has any intentions. So does water run downhill by accident? Well, I would venture that gravity plays a role.

    But wait! Does gravity intend for water to run downhill? I’d have trouble constructing a reasonable phraseto describe gravity having wants, desires, or purposes. But things aren’t attracted by gravity by accident either.

    Surely you yourself could come up with many such examples, of clearly mindless forces or processes nonetheless producing predictable, non-accidental results. Water does not run downhill either on purpose or by accident. Your dichotomy is flawed.

    Well the issue is the term being used is teleology. I don’t think anyone sane uses the term teleological to describe water running downhill, as there is no aim or goal. That’s exactly the point, isn’t it?

    We are talking about when authors or scientists do use the term teleology to describe biological systems. They most definitely don’t mean like water running downhill.

    But some here are now trying to convince us this is what they mean.

  36. DNA_Jock,

    Pleas try to think for held a second. You are trying to say I didn’t want to admit Goodwin believes in alternative science. That’s absurd, I am saying that is exactly what he believes. So what you are saying doesn’t just not make any sense, you are inadvertently confirming what I am saying. That his ideas are no different than the ideas of Sheldrake, whom you consider a crank but for some reason didn’t say this about Goodwin or others who see teleology and morphic fields in biology. If you want to now say you fully believe in morphic fields, I say welcome. Woo is you, congratulations.

    Morphic fields and teleological biology can use more converts like you.

  37. phoodoo: We are talking about when authors or scientists do use the term teleology to describe biological systems. They most definitely don’t mean like water running downhill.

    Agreed, that I would not use “teleology” for water flowing down hill.

    But I also would not use “accidental” or “planned”. So you gave us a false dichotomy.

  38. phoodoo,

    This confusing of several different concepts linked only by a similar etymology borders on (I’m being kind) the disingenuous, phoodoo.

    Morphogenesis is a label for processes observed in developing embryos involving growth, topology and differentiation of cells and groups of cells.

    Morphogenetic field is a somewhat passé term originating in the 1920s, largely superceded since the rôle of hox genes has become better understood.

    Morphic resonance is Rupert Sheldrake’s Idea from 1982 which has remained no more than his speculation since.

  39. phoodoo: You can not talk about biology in any detail at all, without using teleological language. Rummy can’t do it, no one can do it, because it just sounds too ridiculously unbelievable.

    And yet somehow I’ve been doing exactly that, and it sounds fine. But hey, I’m talking to the guy who can’t wrap his head around the concept of natural selection.

  40. On a related note, there is of course another sense in which the concept of existing for a purpose, that is to say having a reason for being in existence, can be explained purely in mechanistic terms without any appeal (nor even implication) to intent or conscious agency. It’s natural selection.

    With natural selection you can say that because of how some entity contributes to reproductive fitness – that explains why it exists. That it’s purely mindless and mechanical effect on reproductive output is the explanation for it’s existence, and hence the purpose(reason for existing) of the entity is the function(s) it performs that directly positively contributes to fitness. No intent, mind, or foresight is implied by that. With natural selection, you can get a sort of “intrinsic purpose”. I concede I have to retract my earlier statement that there could be no such thing. If that is what you mean by purpose, the explanation for why something exists, then you can get that with natural selection.

    That is the genius of Darwin’s concept, that it explains how you can get a “purpose for existing” without intent.

    Somehow phoodoo just remains fantastically wrong on all levels. But again, he doesn’t even know what natural selection is. He literally can’t understand the concept that different organisms can have different reproductive capacities. Some have more offspring than others. The very idea causes a meltdown in his mind.

  41. phoodoo: Well the issue is the term being used is teleology. I don’t think anyone sane uses the term teleological to describe water running downhill, as there is no aim or goal.

    But how do you know there is no aim or goal? Could you not simply say that water running downhill has the goal of forming rivers, lakes, oceans, and to sustain and host ecosystems by providing environments in which certain organisms live? It has the function, the purpose, of washing salts and minerals out of mountains and rocks and carrying it to plants and animals? Could the God you believe in not be intending for these things to happen, and have created the physics that cause water exist and to run downhill for this reason?

    What makes you able to say some adaptation on an organism has a goal, yet water running downhill does not?

  42. Rumraket:
    CharlieM: Looking at translation processes in protein synthesis, the explanation that free floating amino acids just happen to bump into tRNAs which happen to bump into ribosomes becomes so simplified that it is a non-explanation

    Rumraket: No, it doesn’t. That’s false. That free amino acids encounter tRNA-synthetases, which encounter tRNA, which encounters ribosomes really does constitute a part of the explanation for the things that occur during coded protein biosynthesis.

    But it’s not just two molecules that need to come together. Amino acid, ATP, corresponding aminoacyl-tRNA synthetase (a different one for each amino acid) and tRNA all have to be present and available. Only if the amino acid combined with AMP is appropriate for the anti-codon on the tRNA will the aminoacyl-tRNA synthetase attach it to the tRNA. Once this in place it is ready to fill the “A” position of the ribosome complex which has been assembled round the mRNA strand. The ribosome must position itself at the correct point on the mRNA strand in order to accept a suitable charged tRNA to start peptide elongation. Then amino acids must be added in the correct sequence.

    Rumraket: It just doesn’t constitute an explanation for everything that occurs inside the cell. Yes, this process is itself a part of other processes on which it relies. And yet these particular events are still stochastic elements of the process of translation.

    When I was a kid I sometimes dug up lugworms to use as fishing bait. There was a stochastic element to which worms in the area went into my bait tin. But there was an overall intent to the process.

    CharlieM: And we should not forget that all the players in this process must be present and available in the suitable quantities at the right time and place.

    Rumraket: Nobody forgets that.

    But people can become so focused on the details that these things go to the back of their minds.

    CharlieM: This process is fundamental and vital for living systems and no living cell could exist without it.

    Rumraket: That depends on what you define to be a living cell, doesn’t it?

    How about a mixed amphiphile+fatty acid bilayer vesicle powered by a local geologically hosted metabolism, encapsulating a set of collectively replicating ribozymes, yet without coded protein biosynthesis, being based in part on very short but continuously generated set of random-sequence peptides performing rudimentary functions? – That would fail to qualify for your definition of a “living cell” or “living system”(?) because you seem to have merely said that by definition a living cell/system must have coded protein biosynthesis.

    But a system such as the one I described is a candidate stage in the evolution of living cells as we know them. What use is it to declare that such a system is not a form of life, if there really was such a stage in life’s eventual emergence?

    I’m talking about any living cell that we can observe. Not some speculative precursor to known cells.

    Why speculate on a simpler precursor to the cell? Because that is what is needed for the beginning of physical life to be a fortuitous blind search. But what if it wasn’t a fortuitous blind search? There is no known active living systems that exist without the presence of cells. In prokaryotes we have the lowest level of complexity in which life is known to exist.

  43. Neil Rickert: Agreed, that I would not use “teleology” for water flowing down hill.

    But I also would not use “accidental” or “planned”.So you gave us a false dichotomy.

    Of course YOU wouldn’t. But that’s because you have an agenda, like most skeptics.

    But normal people would.

  44. Alan Fox:
    CharlieM: But all this is distracting from understanding the actual processes involved in protein synthesis.

    Alan Fox: There’s always the possibility to start another thread. But ATP is central to protein synthesis providing the necessary energy.

    It’s just that I’m not all that interested if ATP bonds or the bonds they produce are called high energy bonds or not. It’s all relative as far as I’m concerned.

    CharlieM: In my opinion adding enzymes piecemeal to a much simpler system just would not work.

    Alan Fox: Is that just a gut feeling or can you suggest why incremental changes would not work?

    It seems logical to me.

    For instance if a process such as protein building that involves more than a couple of steps and simultaneous operations is to have any success it needs to have everything working in a strict relationship. If an enzyme that vastly increases the rate of charged tRNA production comes along but there are several enzymes involved in ribosome construction that haven’t yet appeared limiting the rate of ribosome construction to a value that isconsiderably lower than at present, what would happen? The cell would start to amass countless charged tRNA complexes unable to proceed to the next stage because there weren’t enough ribosomes ready to accept them. It would be chaos.

    The production of ribosomes:

    involves the coordinated function of over 200 proteins in the synthesis and processing of the three prokaryotic or four eukaryotic rRNAs, as well as assembly of those rRNAs with the ribosomal proteins…

    Ribosome biogenesis is a very tightly regulated process, and it is closely linked to other cellular activities like growth and division.

    Also something to note:

    The accuracy of aminoacyl-tRNA synthetase is so high that it is often paired with the word “superspecificity” when it is compared to other enzymes that are involved in metabolism. Although not all synthetases have a domain with the sole purpose of editing, they make up for it by having specific binding and activation of their affiliated amino acids. Another contribution to the accuracy of these synthetases is the ratio of concentrations of aminoacyl-tRNA synthetase and its cognate tRNA. Since tRNA synthetase improperly acylates the tRNA when the synthetase is overproduced, a limit must exist on the levels of aaRSs and tRNAs in vivo

    Coordinated rates of production are vital to the life of the cell. Whole cell coordination must have been maintained throughout all of their evolutionary history.

  45. Alan Fox:
    phoodoo,

    This confusing of several different concepts linked only by a similar etymology borders on (I’m being kind) the disingenuous, phoodoo.

    Morphogenesis is a label for processes observed in developing embryos involving growth, topology and differentiation of cells and groups of cells.

    Morphogenetic field is a somewhat passé term originating in the 1920s, largely superceded since the rôle of hox genes has become better understood.

    Morphic resonance is Rupert Sheldrake’s Idea from 1982 which has remained no more than his speculation since.

    You are so easily fooled by Jock’s phony blustering. Sheldrake himself says that he got the idea for morphic resonance while thinking about morphogenetic fields. THAT’S why he called it that!

    And since you are so concerned about people’s degress, Sheldrake has better credentials than anyone who ever posted here, that’s for sure.

  46. Rumraket: That is the genius of Darwin’s concept, that it explains how you can get a “purpose for existing” without intent.

    KN, are you paying attention?

    THIS is what most people that believe in evolution cling to. With Darwinism, nothing has intent.

    Its why the idea of teleology is so dangerous to the faithful. It threatens their worldview.

  47. Oh the irony. Here let me correct that.

    phoodoo: Its why the idea of teleology natural selection is so dangerous to the faithful. It threatens their worldview.

  48. CharlieM: But it’s not just two molecules that need to come together. Amino acid, ATP, corresponding aminoacyl-tRNA synthetase (a different one for each amino acid) and tRNA all have to be present and available.

    They don’t have to be present literally simultaneously, amino acid can and will be phosphorylated before being charged to tRNA by the aaRS enzyme.

    Not that any of this implies intent is necessary for this to occur anyway.

    CharlieM:
    Only if the amino acid combined with AMP is appropriate for the anti-codon on the tRNA will the aminoacyl-tRNA synthetase attach it to the tRNA. Once this in place it is ready to fill the “A” position of the ribosome complex which has been assembled round the mRNA strand. The ribosome must position itself at the correct point on the mRNA strand in order to accept a suitable charged tRNA to start peptide elongation. Then amino acids must be added in the correct sequence.

    And?

    CharlieM:
    When I was a kid I sometimes dug up lugworms to use as fishing bait. There was a stochastic element to which worms in the area went into my bait tin. But there was an overall intent to the process.

    Yeah yours, in your head you intended for something to happen. That’s where the intent was. It was nowhere else but an idea you had in your mind. That is to say, in your head. People without heads that contain thinking brains rarely come posting about their intents. I think that’s a hint.

    CharlieM:
    I’m talking about any living cell that we can observe. Not some speculative precursor to known cells.

    And yet you go on to offer that very thing, a speculative precursor to known cells: their creation by a divine being. Something we do not observe and literally can’t be tested by any method.

    CharlieM:
    Why speculate on a simpler precursor to the cell? Because that is what is needed for the beginning of physical life to be a fortuitous blind search.

    No, because the entire history of life testifies to it’s origin from simpler and ultimately dead material things. Life is an emergent physical phenomenon that arose from non-living physical things. I’m sorry but it’s just ALL of science that supports this.

    That life is a physical phenomenon subject to natural law in both it’s constituents and functions(including both the fact that life reproduces and evolves physically), and the historical success of science in explaining the origins and functions of innumerable other physical phenomena relevant to life(including everything from growth and metabolism, to reproduction and behavior) supports the inference life’s origin will also be solved as another physical process eventually.

    Then there’s a broader context of natural history, into which life’s physical and chemical origin sits very well, beginning with the condensation of matter into atoms following big bang nucleosynthesis, producing stars, galaxies, and planets following the universe’s expansion and cooling, that stars churn out the elements of which life is made in large quantities, and that once life existed, it continued to evolve and diversify. This whole picture implies life’s origin is just another “step” or “event” in this extremely long process of physical change and increasing complexity of emergent physical phenomena. At some point the universe contained basically nothing more complex than hydrogen, helium, and beryllium nuclei, and before that it was basically a chaotic soup of subatomic particles. Billions of years later it contained stars, and planets with geology and atmospheres.

    Then there’s more direct evidence from life previously mentioned. Evidence for the existence of an RNA world which you seem to give no explanation for.

    Then there’s evidence in the form of the consilience between the distribution in the frequency of amino acid usage in the most ancient ancestral nodes in the phylogenetic trees of universally conserved proteins, and the kinds of amino acids most abundantly produced in abiotic organic chemistry experiments, and also observed in carbonaceous chondrite meteorites. The further we go back in time, the more the proteins become like the “abiotic” distribution. This same abiotic distribution is also inferred from multiple different methods analyzing genetic code and translation system evolution. The genetic code appears to have begun by using the must abundant abiotically produced amino acids, implying they really were produced abiotically.
    Then there’s the sorts of functions these ancient proteins have (core metabolism, genetic replication, and translation/transcription), the sorts of co-factors they use (inorganic mineral clusters, metals that would be highly abundant on the early Earth, and nucleotide derivatives).

    All of this heavily implies living cells of the sort we see in the world today, originated and evolved through some physical and chemical process we still don’t understand, and at some point went through an RNA-world-like stage with RNA constituting the primary genetic material and being responsible for most catalytic functions.

    All of this supports and compels both the inference that life is an emergent physical phenomenon, and that it has much simpler origins than even the simplest current cells exhibit.

    You explain NONE of this actual evidence that really does exist, and really does cry out for explanation, by invoking this mysterious disembodied intent.

    CharlieM:
    But what if it wasn’t a fortuitous blind search? There is no known active living systems that exist without the presence of cells.

    What if pigs could fly? There no known active disembodied intending mind wishing cells into existence either, and it doesn’t explain the evidence we already have for life’s simpler beginnings.

    So if you’re going to complain that my idea is not good enough because I can’t yet show you a simpler form of life, how am I to react to your complete fantasy with zero explanatory power compelled by literally no evidence at all?

    CharlieM:
    In prokaryotes we have the lowest level of complexity in which life is known to exist.

    This would be a much stronger point if we had reason to believe we had exhaustive (or at least nearly so) knowledge of what kinds of simplicity is possible.

    But we do not.

  49. phoodoo: Its why the idea of teleology is so dangerous to the faithful. It threatens their worldview.

    When will that danger become apparent?

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