Self-Assembly of Nano-Machines: No Intelligence Required?

In my research, I have recently come across the self-assembling proteins and molecular machines called nano-machines one of them being the bacterial flagellum…

Have you ever wondered what mechanism is involved in the self-assembly process?

I’m not even going to ask the question how the self-assembly process has supposedly evolved, because it would be offensive to engineers who struggle to design assembly lines that require the assembly, operation and supervision of intelligence… So far engineers can’t even dream of designing self-assembling machines…But when they do accomplish that one day, it will be used as proof that random, natural processes could have done too…in life systems.. lol

If you don’t know what I’m talking about, just watch this video:

The first thing that came to my mind when I debating the self-assembly process was one of Michael Behe’s books The Edge of Evolution. I wanted to see whether he mentioned any known, or unknown, mechanism driving the self-assembly process of nano-machines, like the flagellum…

In the Edge of Evolution Behe uses an illustration of a self-assembling flashlight, which parts possess the many different types of magnets that only fit the right type of part into it; each part having the affinity for the corresponding magnet…something like that…

It’s not clear to me whether Behe questions that the magnetic attraction is sufficient for the self-assembly of the flagellum (I might have to read the parts of the book on the theme again). Behe seems to question the ability of Darwinian processes to be able to evolve the sequence and the fitting process of each part of the flagellum, by random processes of random mutation and natural selection…

This is what BIOLOGOS have to say on the theme of self-assembly of the flagelum:

“Natural forces work “like magic”

Nothing we know from every day life quite prepares us for the beauty and power of self-assembly processes in nature. We’ve all put together toys, furniture, or appliances; even the simplest designs require conscious coordination of materials, tools, and assembly instructions (and even then there’s no guarantee that we get it right!). It is tempting to think the spontaneous formation of so complex a machine is “guided,” whether by a Mind or some “life force,” but we know that the bacterial flagellum, like countless other machines in the cell, assembles and functions automatically according to known natural laws. No intelligence required.1

Video animations like this one (video no longer available) by Garland Science beautifully illustrate the elegance of the self-assembly process (see especially the segment from 2:30-5:15). Isn’t it extraordinary? When I consider this process, feelings of awe and wonder well up inside me, and I want to praise our great God.

Several ID advocates, most notably Michael Behe, have written engagingly about the details of flagellar assembly. For that I am grateful—it is wonderful when the lay public gets excited about science! But I worry that in their haste to take down the theory of evolution, they create a lot of confusion about how God’s world actually operates.

When reading their work, I’m left with the sense that the formation of complex structures like the bacterial flagellum is miraculous, rather than the completely normal behavior of biological molecules. For example, Behe writes, “Protein parts in cellular machines not only have to match their partners, they have to go much further and assemble themselves—a very tricky business indeed” (Edge of Evolution, 125-126). This isn’t tricky at all. If the gene that encodes the MS-ring component protein is artificially introduced into bacteria that don’t normally have any flagellum genes, MS-rings spontaneously pop up all over the cell membrane. It’s the very nature of proteins to interact in specific ways to form more complex structures, but Behe makes it sound like each interaction is the product of special design. Next time I’ll review some other examples from the ID literature where assembly is discussed in confusing or misleading ways.”

To me personally, the self-assembly process, especially that of the molecular nano-machines like the bacterial flagellum, involves much, much more than random motion of molecules and the affinity of their binding sites for one another…

There has to be not only some kind of energy directing force but also some hidden information source to direct that energy…I have a hunch what that could be and there is only one way of finding it out…

Does anybody know what I have in mind? No, I don’t think it’s Jesus …

 

471 Replies to “Self-Assembly of Nano-Machines: No Intelligence Required?”

  1. newton
    Ignored
    says:

    Mung:
    …object-oriented software fails when the act of design is separated from the act of programming. Design is process of progressive discovery that relies on a feedback loop.

    – Sandi Metz

    Also known as trial and error or perhaps natural selection.

  2. Corneel Corneel
    Ignored
    says:

    CharlieM: I’m curious to know people’s opinions on the following:

    Other than the scale, what are the differences (fundamental rather than incidental) between the actions of these “nano-beings”, leaf cutter ants transporting their loads to and from their nests, bowerbirds bringing items to their bowers, or humans moving packages around for distribution?

    The difference between the first and the latter three is behaviour. The way organisms respond to internal and external stimuli is unlike the dynamics of biomolecules.

    Not sure where you are going with this. Are you implying that dyneins are alive in the same sense that conscious animals are?

    CharlieM: Yes it is reasonable to say there are different levels of intelligence and awareness between these creatures. So you wouldn’t disagree that there has been an evolution of consciousness?

    I wouldn’t. If that’s your take, then why is it so hard to accept that an animal that creates a pretty pattern hasn’t necessarily planned its design?

  3. newton
    Ignored
    says:

    Corneel: Are you complicating things again?

    I guess so. Like the philosopher Mike Tyson said “ everyone has a plan until they get punched in the mouth ” when he paraphrased Robert Burns”

    But Mousie, thou art no thy lane,
    In proving foresight may be vain:
    The best-laid schemes o’ mice an’ men
    Gang aft agley,

    Just to make sure I understand: you are not referring to just the assembly process, but to using the feedback to adjust the resulting structure, right? Say a spider that makes her web fit to some particular nook?

    Correct, the lines between assembly and design are not always distinct.

  4. Corneel Corneel
    Ignored
    says:

    CharlieM: Me: I believe you considered things to be designed if you could see their purpose. What is Robot B’s purpose?

    Charlie: No I would consider anything with a pattern to be designed. I think of everything from spiral galaxies to frost patterns on a window pane as natural designs. So I like to discuss the source and cause of designs as well as the designs themselves.

    Then you’ve changed your tune. You said bacterial flagella looked designed to you because you could see their purpose. But now you consider everything with a pattern to be designed regardless of whether it serves a purpose? Does that mean that you believe that the construction of all possible patterns was planned, like Robot B was, or do you mean something else by that?

  5. Corneel Corneel
    Ignored
    says:

    newton: Correct, the lines between assembly and design are not always distinct.

    That’s not the way I would use the word, but I am fine with that. Under that definition of design, bowerbirds, spiders and wee mousies truly contribute to the design of their structures. More interesting, evolution by natural selection may also qualify as design. Not sure that is satisfactory to Charlie or J-Mac.

  6. BruceS
    Ignored
    says:

    Alan Fox:

    Alan F:Self-assembly doesn’t involve design. Self-assembly is consequent upon the inherent properties of molecules: their physical properties,

    OP: There has to be not only some kind of energy directing force but also some hidden information source to direct that energy…

    Well, I think it is more than their physical properties. ETA: Specifically, those properties must be leveraged by a set of mechanisms; that is they must be organized in the right way to accomplish a linked set of requirements.

    I think that the theory of that more, that is the requirements and resulting architectures for those mechanisms, is reasonably well understood. Further, contra the OP, no hidden information source at all.
    I won’t pull a KeithS and quote my original post and von Neumann’s theoretical solution to the issue and the mapping of that theory to self-assembly in cells, but it is on the first page of comments…
    http://theskepticalzone.com/wp/self-assembly-of-nano-machines-no-intelligence-required/comment-page-1/#comment-237868

  7. Allan Miller
    Ignored
    says:

    Mung: Which kind?

    http://www.petwebsite.com/hamsters/hamster_species.asp

    The world-controlling kind.

  8. Alan Fox Alan Fox
    Ignored
    says:

    Corneel:…evolution by natural selection may also qualify as design.

    It does! ID proponents have appropriated a perfectly good word for their nefarious purposes. The environment, the niche (and feedback between the niche and its occupant) is a designer.

  9. Alan Fox Alan Fox
    Ignored
    says:

    BruceS,
    Don’t disagree with what you wrote in the linked comment (assuming your use of language and my comprehension are attuned enough for effective communication).

    However…

    Well, I think it is more than their physical properties. ETA: Specifically, those properties must be leveraged by a set of mechanisms; that is they must be organized in the right way to accomplish a linked set of requirements.

    Let me try an analogy that’s just occurred to me. A shepherd, a sheepdog, sheep, a field. The shepherd wants to collect and move the sheep to another field. The dog, to some extent works for the shepherd to the same end, but selective breeding over centuries has resulted in border collies having inherent properties that make them excellent herders both in the absence of shepherds and the absence of sheep. Sheep ditto. They will bunch if approached by a dog. Fields have fences and gates. The shepherd could achieve little or nothing without the inherent properties of dogs, sheep and fields.

    ETA this is a poor analogy in comparison to the physical and chemical properties of bio-molecules, whose properties are fixed for the life of this universe, though evolution can select alternative bio-molecules with more advantageous properties.

  10. Allan Miller
    Ignored
    says:

    I’m still not sure why any concession on the matter of Design by bower birds should lead us anywhere regarding the design of bower birds, or parts thereof.

    Let’s also not forget the role of females here. Birds whose bowers are poor affairs, in the eyes of females, leave fewer offspring. This would tend to optimise ‘designs’, not through any choice on either part, but by the very distortion of allele frequencies that, it is felt, occurs but is trivial. Preference for a particular kind of bower, and the tendency to build that kind of bower, spread through the population in tandem. Males also have daughters, females also have sons.

    The Sheldrakean idea in opposition to this – that male birds are tapping into something in the ether, their shared ancestry and environmental fit somehow an irrelevance, seems ludicrous to me.

  11. BruceS
    Ignored
    says:

    Alan Fox:
    BruceS,
    Don’t disagree with what you wrote in the linked comment (assuming your use of language and my comprehension are attuned enough for effective communication).

    ETA this is a poor analogy in comparison to the physical and chemical properties of bio-molecules, whose properties are fixed for the life of this universe, though evolution can select alternative bio-molecules with more advantageous properties.

    OK, but the deeper point as I see it is that there is that von Neumann provides a functional architecture for self-assembly which is independent of the causal properties of any particular realization of that architecture.

    FWIW, another reason to fear AI: not only can it design smarter versions, but it can use von Neumann’s architecture to make them self-replicating. Only way for us to outsmart it, aside from joining as per Musk, is to use genetic engineering to do the same thing!

  12. Alan Fox Alan Fox
    Ignored
    says:

    Allan Miller:…any concession…

    No concessions!

  13. Alan Fox Alan Fox
    Ignored
    says:

    BruceS: Only way for us to outsmart it, aside from joining as per Musk, is to use genetic engineering to do the same thing!

    Only one way to do that. Emulate evolution!

  14. Alan Fox Alan Fox
    Ignored
    says:

    Allan Miller: Birds whose bowers are poor affairs, in the eyes of females, leave fewer offspring.

    I recall one of the recent BBC Attenborough programs where they observed a particular male Bird of Paradise who managed to attract six females to his display arena and managed to mate with all six. There’s some incentive to outdo your rivals.

  15. Alan Fox Alan Fox
    Ignored
    says:

    *Looks at clock and to-do-list* Have to go.

  16. BruceS
    Ignored
    says:

    newton:
    Correct, the lines between assembly and design are not always distinct.

    I think we can separate them:
    1. Self-assembly only via via replication as per von Neumann’s theory.
    2. Allowing for errors in above process,
    3. Introducing evolutionary mechanisms, including but not limited to NS, which can lead to appearance of design in subsequent populations of replicated individuals.

    Appearance of design occurs with introduction of 2 and 3. Design requiring intelligence is replacing 2 by intelligent engineering.

    BTW I think “appearance of design” is better than “design” just to avoid people who assume “design” implies intelligence.

  17. DNA_Jock
    Ignored
    says:

    Allan Miller,

    Glad I wasn’t the only one to read that and think “Woooh! Sheldrake!”
    I also enjoyed the phermone question:

    They are species specific, so presumably a change in the female’s signalling pheromone would need to be accompanied by an equivalent change in the receiving apparatus of the male moth if there is to be any mating.

    which reminded me of the RayComfortesque “cats giving birth to dogs, who then have no-one to fuck” objection to speciation.
    Charlie, what do you think might happen within a species if different female moths produced different mixtures of phermones, and different male moths preferred different smells? Over the long haul?

  18. CharlieM CharlieM
    Ignored
    says:

    newton:

    CharlieM: The urge to build bowers is instinctive, but the actual construction depends on the whims of the individual bowerbird and the available materials. I don’t really care if we describe bowerbirds as designers, architects or builders.

    The problem with that position for ID is it opens up design to non intelligent processes such as evolution.

    Well I think that the amount of intelligence there is in evolution is the question that is being asked. We should not just assume that it is a non-intelligent process.

    It is possible that natural selection acting on chance variables has the power to produce the advanced forms of life capable of observing themselves. But IMO the new evidence coming to light makes that look more and more unlikely. The amount of integrated, cooperative processes being undertaken at the nano-scale, in order to keep higher organisms alive and functioning, is being revealed to be of an organisation scarcely imagined not so many decades ago.

  19. Allan Miller
    Ignored
    says:

    Alan Fox: No concessions!

    Indeed – I only make the for the sake of argument! I just wonder where the concession, if granted, is supposed to lead us.

  20. CharlieM CharlieM
    Ignored
    says:

    Corneel:

    CharlieM: I’m curious to know people’s opinions on the following:

    Other than the scale, what are the differences (fundamental rather than incidental) between the actions of these “nano-beings”, leaf cutter ants transporting their loads to and from their nests, bowerbirds bringing items to their bowers, or humans moving packages around for distribution?

    The difference between the first and the latter three is behaviour. The way organisms respond to internal and external stimuli is unlike the dynamics of biomolecules.

    Dynein nano-beings are capable of varied responses to obstacles on their path.

    What in your opinion causes them to pick up a load and walk along microtubules?

    Not sure where you are going with this. Are you implying that dyneins are alive in the same sense that conscious animals are?

    All four of my examples are alive. But you have revealed an important distinction and that is the level of consciousness varies between the examples.

  21. CharlieM CharlieM
    Ignored
    says:

    Corneel:

    Charlie: No I would consider anything with a pattern to be designed. I think of everything from spiral galaxies to frost patterns on a window pane as natural designs. So I like to discuss the source and cause of designs as well as the designs themselves.

    Then you’ve changed your tune. You said bacterial flagella looked designed to you because you could see their purpose. But now you consider everything with a pattern to be designed regardless of whether it serves a purpose? Does that mean that you believe that the construction of all possible patterns was planned, like Robot B was, or do you mean something else by that?

    I haven’t said they looked designed because they seemed to have a purpose. I may have said that, unlike leopards or fish, they appear to be designed for a purpose, because we can see the purpose they serve. I have made a distinction between “designed” and “designed for a purpose”.

  22. Allan Miller
    Ignored
    says:

    CharlieM:

    I think we’re arguing semantics here.

    Not if you are trying to make it part of a case on capital-D Design. You obviously think it important.

    But I do think it highlights the difference between instinctive behaviour determined by the group and the actions of individuals within the group.

    This actually highlights indicates your unwillingness to grasp another potential cause of ‘group’ behaviour – common descent. If all organisms share an instinctive behaviour, common descent (of the trait) is probably a better explanation than telepathy or similar, IMO.

    Individual moths do not design pheromones but they do build them, just as they build muscles, bones and feathers.

    Moths with muscles, bones and feathers? Are you sure they’re moths? 😀

    On the subject of pheromones, how do you think that they change by the process of natural selection? They are species specific, so presumably a change in the female’s signalling pheromone would need to be accompanied by an equivalent change in the receiving apparatus of the male moth if there is to be any mating.

    I think it’s necessary to dispense with dichotomous, ‘all-or-nothing’ thinking. You might have discovered a principle that precludes the evolution of any complementary feature between males and females – for example the respective sex organs involved in internal fertilisation – but you probably haven’t. If there is latitude – variation – then two characters can covary, and track each other, rather than each being perpetually pinned in place by the other. The same applies in other arenas where complementarity exists – binding sites, for example.

    I would say that rather than making anything, natural selection changes the composition of groups in line with prevailing conditions. Individuals vary within groups and natural selection changes the distribution of this variation.

    But how? What is the causal reason why NS changes distributions? What distinguishes it from Drift?

    eta – well, you kind of already answered – ‘in line with prevailing conditions’. But this is hardly nothing. It is a process that increases the frequency of variants with a better fit to the environment – as if by Design.

  23. Corneel Corneel
    Ignored
    says:

    Alan Fox: ID proponents have appropriated a perfectly good word for their nefarious purposes.

    Hm, let me suggest as a non-native speaker that the word was a bit promiscuous to start with.

  24. Corneel Corneel
    Ignored
    says:

    CharlieM: Dynein nano-beings

    You want me to seriously discuss this?

    CharlieM: All four of my examples are alive.

    We’ll continue this discussion once you show me little dynein nano-babies

  25. Corneel Corneel
    Ignored
    says:

    CharlieM: I haven’t said they looked designed because they seemed to have a purpose. I may have said that, unlike leopards or fish, they appear to be designed for a purpose, because we can see the purpose they serve. I have made a distinction between “designed” and “designed for a purpose”.

    OK, I see. But I am still curious about the answer to my question:

    Does that mean that you believe that the construction of all possible patterns was planned, like Robot B was, or do you mean something else by that?

  26. CharlieM CharlieM
    Ignored
    says:

    Allan Miller:
    I’m still not sure why any concession on the matter of Design by bower birds should lead us anywhere regarding the design of bower birds, or parts thereof.

    Let’s also not forget the role of females here. Birds whose bowers are poor affairs, in the eyes of females, leave fewer offspring. This would tend to optimise ‘designs’, not through any choice on either part, but by the very distortion of allele frequencies that, it is felt, occurs but is trivial. Preference for a particular kind of bower, and the tendency to build that kind of bower, spread through the population in tandem. Males also have daughters, females also have sons.

    The Sheldrakean idea in opposition to this – that male birds are tapping into something in the ether, their shared ancestry and environmental fit somehow an irrelevance, seems ludicrous to me.

    You say that the behaviour of bowerbirds is genetic. So which genes are causing this behaviour?

  27. Mung Mung
    Ignored
    says:

    Alan Fox: Self-assembly doesn’t involve design. Self-assembly is consequent upon the inherent properties of molecules: their physical properties, their chemical properties, how they attract or repel, where with what strengths, react with water, in water, pH, ionic concentration and so on. None of this can be designed; it gets taken advantage of in design processes like adaptation.

    You’re begging the question. How do you know none of that can be designed?

  28. CharlieM CharlieM
    Ignored
    says:

    Alan Fox: I recall one of the recent BBC Attenborough programs where they observed a particular male Bird of Paradise who managed to attract six females to his display arena and managed to mate with all six. There’s some incentive to outdo your rivals.

    It may be a bit more complex than you think.

    Thus, bowerbirds may use a diversity of auditory, chemical and visual cues to select mates. These results and those of Coleman et al. (2004) show that mate choice in satin bowerbirds is extremely complex and that this species is an ideal subject for the study of the evolution of multiple signals.

  29. CharlieM CharlieM
    Ignored
    says:

    DNA_Jock: Charlie, what do you think might happen within a species if different female moths produced different mixtures of phermones, and different male moths preferred different smells? Over the long haul?

    I’m not talking about the long haul. Can you run us through the genetic changes in both sexes after a female moth begins sending out a pheromone which has changed due to a mutation?

    What ensures that the male moth will suddenly be attracted to the altered pheromone?

  30. DNA_Jock
    Ignored
    says:

    CharlieM: I’m not talking about the long haul. Can you run us through the genetic changes in both sexes after a female moth begins sending out a pheromone which has changed due to a mutation?

    In the “short haul”, there will be no genetic changes. Over a number of generations, allele frequencies will change.

    What ensures that the male moth will suddenly be attracted to the altered pheromone?

    Nothing.
    This is the Ray-Comfortesque IDiotrope that I was lampooning: “If a cat gave birth to a dog, how could this, the only dog, mate? Huh? How? Yeah!”.

    Onwards to the actual biology.
    The first thing to recognize is that moths are diploid. If a female gets a mutation [A->B] that alters pheromone production, she will be heterozygous A/B, and her phenotype may be somewhere in between A/A and B/B. Likewise for male receptors, see below.
    The second thing to recognize is that mutations do not have to be all-or-nothing, especially the receptors, where different versions will have varying (non-zero) affinities for different pheromones.
    Thirdly, even homozygous moths produce a mixture of pheromones (typically related via chain-shortening…)
    So your “hopeful monster” scenario does not impede the evolution of moth pheromones. At all.
    But here’s the fun thing (and it’s why I enjoy this place so…):
    When I made my original comment about “Charlie, what do you think would happen if…” I was merely encouraging you to ponder a hypothetical and perhaps improve your understanding as a result. Maybe Charlie would see that a divergence of signalling signals could lead to speciation. As my Mum would say, “Hope springs eternal…”.
    At the time, I did not realize that exactly the type of saltation that Charlie views as impossible is, in fact, responsible for the speciation of the Asian Corn Borer (ACB) moth!
    European Corn Borer (ECB) females use a Δ11 desaturase to make pheromones, whereas, uniquely ACBs use a Δ14 desaturase. It’s a non-overlapping set of pheromones!
    But guess what? There’s a subset of ECB males who respond (and respond well…) to the ACB pheromones. Thus explaining how the “saltation” could occur.
    [Also supporting gradualism, there are strains of ECBs that respond differently to different E/Z isomer mixtures of the ECB pheromones.
    F1 hybrids show inter-fucking-mediate responses to the different E/Z isomer mixtures.]
    This stuff is way cool.
    P.S. If someone decides to quote-mine the linked article, I have a more recent reference that will stuff them up but good. It’s a trap!

  31. Allan Miller
    Ignored
    says:

    CharlieM: You say that the behaviour of bowerbirds is genetic. So which genes are causing this behaviour?

    Does it actually matter? Would you be preparing a salvo along the lines that, if I don’t know the DNA sequences, it’s not genetic? That would preclude nearly all pre-1980 genetics, for starters.

  32. CharlieM CharlieM
    Ignored
    says:

    Allan Miller:

    I think we’re arguing semantics here.

    Not if you are trying to make it part of a case on capital-D Design. You obviously think it important.

    I am only interested in design as it relates to the wisdom found in nature, whether instinctive wisdom or conscious wisdom. And we see the distinction between the two when we compare examples of innate behaviour and of learned behaviour.

    But I do think it highlights the difference between instinctive behaviour determined by the group and the actions of individuals within the group.

    This actually highlights indicates your unwillingness to grasp another potential cause of ‘group’ behaviour – common descent. If all organisms share an instinctive behaviour, common descent (of the trait) is probably a better explanation than telepathy or similar, IMO.

    If, for example, you want to attribute to common descent the migration of Monarch butterflies, or the round trips made by European eels, then can you provide the evidence for this? What genes do you think are involved in this behaviour, and how instrumental are they in causing this behaviour?

    I have never proposed telepathy as a cause.

    Individual moths do not design pheromones but they do build them, just as they build muscles, bones and feathers.

    Moths with muscles, bones and feathers? Are you sure they’re moths?

    Oops, in my rush I meant to amend “just as they”, to “just as birds” and I forgot.

    On the subject of pheromones, how do you think that they change by the process of natural selection? They are species specific, so presumably a change in the female’s signalling pheromone would need to be accompanied by an equivalent change in the receiving apparatus of the male moth if there is to be any mating.

    I think it’s necessary to dispense with dichotomous, ‘all-or-nothing’ thinking. You might have discovered a principle that precludes the evolution of any complementary feature between males and females – for example the respective sex organs involved in internal fertilisation – but you probably haven’t. If there is latitude – variation – then two characters can covary, and track each other, rather than each being perpetually pinned in place by the other. The same applies in other arenas where complementarity exists – binding sites, for example.

    The evolution of sex would be an interesting topic on its own.

    So the female moths have unexpressed genes that if turned on allow for a variation in the pheromones they emit and a few of the males will be attracted to this pheromone. This looks to me like a built-in variability within the species, and plasticity has its advantages. Another demonstration of the wisdom in nature.

    I would say that rather than making anything, natural selection changes the composition of groups in line with prevailing conditions. Individuals vary within groups and natural selection changes the distribution of this variation.

    But how? What is the causal reason why NS changes distributions? What distinguishes it from Drift?

    eta – well, you kind of already answered – ‘in line with prevailing conditions’. But this is hardly nothing. It is a process that increases the frequency of variants with a better fit to the environment – as if by Design.

    No, you’re correct, its not nothing. It demonstrates a certain amount of plasticity which is a wise thing to have when everything around you is in a state of flux..

  33. CharlieM CharlieM
    Ignored
    says:

    Corneel: We’ll continue this discussion once you show me little dynein nano-babies

    And maybe you can show me little e-coli babies, or archaea babies 🙂

  34. CharlieM CharlieM
    Ignored
    says:

    Corneel: Does that mean that you believe that the construction of all possible patterns was planned, like Robot B was, or do you mean something else by that?

    As I already implied, spiral galaxies and frost patterns on a window are examples of designs that aren’t planned but are formed due to their intrinsic nature.

  35. newton
    Ignored
    says:

    CharlieM: As I already implied, spiral galaxies and frost patterns on a window are examples of designs that aren’t planned but are formed due to their intrinsic nature.

    Or the nature of the environment in which they exist.

  36. CharlieM CharlieM
    Ignored
    says:

    DNA_Jock:

    CharlieM: I’m not talking about the long haul. Can you run us through the genetic changes in both sexes after a female moth begins sending out a pheromone which has changed due to a mutation?

    In the “short haul”, there will be no genetic changes. Over a number of generations, allele frequencies will change.

    Surely a mutation is a genetic change?

    What ensures that the male moth will suddenly be attracted to the altered pheromone?

    Nothing.
    This is the Ray-Comfortesque IDiotrope that I was lampooning: “If a cat gave birth to a dog, how could this, the only dog, mate? Huh? How? Yeah!”

    You cannot compare change in one pheromone with the change in a complete animal type.

    I’ll respond to the rest of your post once I’ve found the time to go over it and the link you provided. It deserves a closer look than I can give it at the moment.

  37. DNA_Jock
    Ignored
    says:

    CharlieM: Surely a mutation is a genetic change?

    Yes, it most certainly is. You, however, asked about genetic changes that occur after a female moth begins sending out a pheromone which has changed due to a mutation. I answered the question that you asked. Please pay attention.

  38. Allan Miller
    Ignored
    says:

    CharlieM:
    I am only interested in design as it relates to the wisdom found in nature, whether instinctive wisdom or conscious wisdom.

    Surely that’s just more semantics? Is a cold period ‘wise’ because it results in an increase in the frequency of organisms better able to withstand it? Is a population ‘wise’ because it adjusts its membership in response?

    If, for example, you want to attribute to common descent the migration of Monarch butterflies, or the round trips made by European eels, then can you provide the evidence for this? What genes do you think are involved in this behaviour, and how instrumental are they in causing this behaviour?

    Ah, this is familiar territory. I must provide chapter and verse – genetic sequence, mode of implementation, evolutionary history – while all you need to do is waft your arms in the general direction of ‘wisdom’.

    I have never proposed telepathy as a cause.

    Not as such, but you evidently think butterfly minds are tapping into something

    The evolution of sex would be an interesting topic on its own.

    Indeed

    This looks to me like a built-in variability within the species, and plasticity has its advantages. Another demonstration of the wisdom in nature.

    What about novel mutations, or loss of old variants? It’s not just some vague wibbling about a mean; there is an arrow to evolution. But I suspect that this would be ‘wisdom’ too – the Electric Monk again; everything’s a nice shade of Perfect Pink.

  39. Mung Mung
    Ignored
    says:

    Design is more the art of preserving changeability than it is the act of achieving perfection.

    – Sandi Metz

  40. J-Mac
    Ignored
    says:

    The self-assembly issue can be easily resolved and at pretty low cost… If the flagellum requires quantum information to self-assemble, when the QI is disrupted it will not perform all the actions needed…The many experimental scientists posting here should have some insight into this…shouldn’t they?

    BTW: The effects or the influence of the undetectable forces, such as DARK ENERGY, can’t be detected…yet…

  41. Corneel Corneel
    Ignored
    says:

    CharlieM: And maybe you can show me little e-coli babies, or archaea babies 🙂

    All living things reproduce, including Escherichia coli and achaeans. Proteins like dynein do not. Hence they are not living things in themselves, despite the fact that they put you in mind of a pair of jolly little legs.

  42. Corneel Corneel
    Ignored
    says:

    CharlieM: As I already implied, spiral galaxies and frost patterns on a window are examples of designs that aren’t planned but are formed due to their intrinsic nature.

    Yes, that is what I expected. That’s fine, but then you are using the word design in another way then I do and, I believe, most other people here at TSZ, including the pro-ID crowd.

  43. CharlieM CharlieM
    Ignored
    says:

    DNA_Jock: Onwards to the actual biology.
    The first thing to recognize is that moths are diploid. If a female gets a mutation [A->B] that alters pheromone production, she will be heterozygous A/B, and her phenotype may be somewhere in between A/A and B/B. Likewise for male receptors, see below.
    The second thing to recognize is that mutations do not have to be all-or-nothing, especially the receptors, where different versions will have varying (non-zero) affinities for different pheromones.
    Thirdly, even homozygous moths produce a mixture of pheromones (typically related via chain-shortening…)

    For female sex pheromones to be effective they need to be species specific. Moths achieve this by varying the constitution of fatty-acid precursors and blending the products in differing proportions, and thus enabling them to release a mixture which is unique to the species. European corn borers (ECB) and Asian corn borers (ACB) both contain transcripts of three different desaturase genes including those for Δ11-desaturase and for Δ14-desaturase. While both species have these genes the ECB expresses Δ11-desaturase and the ACB expresses Δ14-desaturase.

    So both species have the genes for producing the same pheromones but use them in differing ways. And both species can interbreed, but the preference of the males for the specific pheromones keeps them from doing so. This is where the concept of species becomes fuzzy.

    So your “hopeful monster” scenario does not impede the evolution of moth pheromones. At all.
    But here’s the fun thing (and it’s why I enjoy this place so…):
    When I made my original comment about “Charlie, what do you think would happen if…” I was merely encouraging you to ponder a hypothetical and perhaps improve your understanding as a result. Maybe Charlie would see that a divergence of signalling signals could lead to speciation. As my Mum would say, “Hope springs eternal…”.

    I wasn’t proposing any “hopeful monster” scenario. What your comment did do was encourage me to look more closely at pheromone production in moths, so I am grateful for that.

    At the time, I did not realize that exactly the type of saltation that Charlie views as impossible is, in fact, responsible for the speciation of the Asian Corn Borer (ACB) moth!

    I don’t recall saying that anything was impossible.

    European Corn Borer (ECB) females use a Δ11 desaturase to make pheromones, whereas, uniquely ACBs use a Δ14 desaturase. It’s a non-overlapping set of pheromones!
    But guess what? There’s a subset of ECB males who respond (and respond well…) to the ACB pheromones. Thus explaining how the “saltation” could occur.
    [Also supporting gradualism, there are strains of ECBs that respond differently to different E/Z isomer mixtures of the ECB pheromones.
    F1 hybrids show inter-fucking-mediate responses to the different E/Z isomer mixtures.]
    This stuff is way cool.
    P.S. If someone decides to quote-mine the linked article, I have a more recent reference that will stuff them up but good. It’s a trap!

    Everything about these pheromones is complex. From their production, their dispersal to the way in which males pick up the signal and respond, it is all a very complicated set of interactions which is still not fully understood.

    The Genetic Basis of Pheromone Evolution in Moths

    Traditionally, moth sexual pheromones have been studied as a static, fine-tuned system of intraspecific sexual communication that reinforces interspecific reproductive isolation. Most studies have focused on long-range attraction of males to female-emitted pheromones; the close-range attraction of females to male-emitted pheromones has received much less attention. The female signal is unimodal and exclusively chemical, produced in a well-defined gland, and readily quantified. The male behavioral response is robust and specific, and the well-studied pheromone sensory system serves as an important model for decoding olfactory preference in general. However, although female sex pheromones of >1,600 moth species have been enumerated, the dynamic mechanisms of evolutionary change at work in pheromone systems are still obscure: How the female signal and male preference can concomitantly change remains a dilemma. To resolve this problem, researchers must identify the genes responsible for intraspecific variation in and interspecific divergence of the pheromone system. However, so far, only five such genes have been identified.

  44. CharlieM CharlieM
    Ignored
    says:

    newton: Or the nature of the environment in which they exist.

    Well I wouldn’t say “or”, I would say “and”. But thank you for pointing that out. Looking at things in isolation will not give us their real natures. Everything around us must be seen in relation to something else.

  45. CharlieM CharlieM
    Ignored
    says:

    DNA_Jock: Yes, it most certainly is. You, however, asked about genetic changes that occur after a female moth begins sending out a pheromone which has changed due to a mutation. I answered the question that you asked. Please pay attention.

    Well I try to give it as much attention as I can afford. But at least I can be safe in the knowledge that any slip ups I make will be quickly pointed out to me, so that I can correct the error of my ways 🙂

  46. Corneel Corneel
    Ignored
    says:

    CharlieM: So both species have the genes for producing the same pheromones but use them in differing ways. And both species can interbreed, but the preference of the males for the specific pheromones keeps them from doing so. This is where the concept of species becomes fuzzy.

    Do you have an explanation for the rare ECB males that were responsive to the blend of the asian species? Perhaps they had a little interference when communicating with their group souls?

  47. CharlieM CharlieM
    Ignored
    says:

    Allan Miller: Surely that’s just more semantics? Is a cold period ‘wise’ because it results in an increase in the frequency of organisms better able to withstand it? Is a population ‘wise’ because it adjusts its membership in response?

    We can attribute wisdom to living beings, not events.

    Ah, this is familiar territory. I must provide chapter and verse – genetic sequence, mode of implementation, evolutionary history – while all you need to do
    is waft your arms in the general direction of ‘wisdom’.

    Anyone who wants to demonstrate the causal power of genes has no option but to at least provide evidence as to which genes are responsible for the effect in question.

    CharlieM: I have never proposed telepathy as a cause.

    Not as such, but you evidently think butterfly minds are tapping into something

    Neither have I mentioned butterfly minds. The behaviour of these butterflies is sufficient for me to consider the group as an individual entity made up of separate organsims, in the same way that the heart can be considered as an individual entity made up of cardiac cells. The wisdom inherent in the structure of termite mounds cannot be found within individual termites, nor in any part therein,, it is a group wisdom, realized by group action.

    Indeed

    What about novel mutations, or loss of old variants? It’s not just some vague wibbling about a mean; there is an arrow to evolution. But I suspect that this would be ‘wisdom’ too – the Electric Monk again; everything’s a nice shade of Perfect Pink.

    Good to see you saying there is an arrow to evolution 🙂

    Nothing is predestined to achieve its potential, neither in life as a whole nor in individual organisms. “Mutations” such as gene duplications are important to allow for plasticity. The wisdom is in providing multiplicity in order to ensure future viability. Natural systems use randomness and determinism in combination to ensure future viability. For example there is randomness about plant seed distribution but they are produced in enough numbers to ensure that a percentage of them will grow and produce the next generation of the parent plant.

  48. CharlieM CharlieM
    Ignored
    says:

    J-Mac:
    The self-assembly issue can be easily resolved and at pretty low cost… If the flagellum requires quantum information to self-assemble, when the QIis disrupted it will not perform all the actions needed…The many experimental scientists posting here should have some insight into this…shouldn’t they?

    BTW: The effects or the influence of the undetectable forces, such as DARK ENERGY, can’t be detected…yet…

    I noticed that quantum information is briefly mentioned in an article Allan Miller linked to in your recent thread on information

    The theoretical modeling of specific polymerases thus represents a physical basis to connect classical information processing in biological systems to artificial, nanoscale platforms, and to open promising avenues in quantum information copying strategies.

    I would also like to hear what the experts say about quantum information in relation to flagellar self assembly or polymerases but no scientist here seems willing to discuss this with you J-Mac.

  49. CharlieM CharlieM
    Ignored
    says:

    Corneel: All living things reproduce, including Escherichia coli and achaeans. Proteins like dynein do not.Hence they are not living things in themselves, despite the fact that they put you in mind of a pair of jolly little legs.

    A “dynein being” is composite, it is not just a protein but a complex of proteins. When does something become a living thing in itself? Are all the social insect workers that do not reproduce excluded from being classed as living things because of this? What about slime molds? Are the individual cells living things or is it just when they aggregate they become living things?

  50. Allan Miller
    Ignored
    says:

    CharlieM: We can attribute wisdom to living beings, not events.

    Well, slowly but surely you are clarifying your terms. Are you saying that, when you talk about the wisdom of nature, that nature is a living being?

    My point still stands, I think. If a population adapts by a change in frequency of favourable traits, where is ‘wisdom’ applied? What’s its mode of operation, and how can it be distinguished from that which evolutionists term ‘adaptation’?

    Anyone who wants to demonstrate the causal power of genes has no option but to at least provide evidence as to which genes are responsible for the effect in question.

    Anyone who wants to bring an alternative explanation to bear might consider themselves held to their own standard, in fairness.

    Me:Not as such, but you evidently think butterfly minds are tapping into something

    Charlie: Neither have I mentioned butterfly minds. The behaviour of these butterflies is sufficient for me to consider the group as an individual entity […]

    So how does that assumed entity persuade the individual butterflies to flap their little wings and head south?

    The wisdom inherent in the structure of termite mounds cannot be found within individual termites, nor in any part therein,, it is a group wisdom, realized by group action.

    Do you think that the cells of a single body are exhibiting ‘group wisdom’?

    Good to see you saying there is an arrow to evolution

    That does not mean what you think it means.

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