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 …
Is that a “yes” or a “no”?
It seems to be a “yes”.
I am merely trying to understand what you are trying to say. Agreement or disagreement can only come AFTER comprehension.
Are you saying that
1) humans do consciously control our molecular processes, and
2) that materialists cannot come to grips with this fact.
Dennett on Magic and Understanding Consciousness.
[start of quote]
I [a stage magician talking to Dennett] am writing a book on magic, I explain, and I’m asked, Real magic? By real magic people mean miracles, thaumaturgical acts, and supernatural powers. No, I answer: Conjuring tricks, not real magic. Real magic, in other words, refers to the magic that is not real, while the magic that is real, that can actually be done, is not real magic.
Yes we do have that in common.
Well, for instance, would you say that someone who believes that there is truth in Christianity or Islam because of their culture and upbringing is the same as someone who comes to their beliefs through personal effort and enquiry?
Yes both of their temperaments allowed them to be able to regard views that differed from their own with a certain understanding.
And the worse thing that can happen is that those differences lead to prejudice against the other person.
So we are both getting something out of contributing, that’s good 🙂
I said exactly what I said. Its too complicated for you?
Humans can make conscious decisions which affect the state of the chemicals that humans are consisted of.
Real magic is not real magic. So the only real magic is fake magic?
And people wonder why people like phoodoo and I exist.
and yet CharlieM wrote:
[Errr. No one except phoodoo, that is…]
Allan’s point, and mine, was that the evolution-deniers around here spectacularly fail to pick up on disagreements they have with each other. For maximum lulz, he made his observation in the comment immediately preceding your “Did you even watch the video? It has nothing whatsoever to do with defining machines. Its about how through conscious will, we change the length of the telomeres in your DNA.” rant.
I particularly enjoyed the repetition of the “Did you even watch the video?” question.
So the original “Whoosh” was the sound of phoodoo’s claim going over Charlie’s head. But, irony of ironies, phoodoo fails to see this, and misconstrues my comment altogether.
Cool story bro.
What causes those decisions?
Is it molecules?
So humans, who consist of chemicals, make conscious decisions which affect the state of chemicals that humans consist of. Where does the non-material come in?
I would not class myself as an evolution doubter.
To understand where phoodoo and myself are coming from it just takes is a bit of charitable reading. Unless we have superpowers or we have access to a marvellous piece of equipment that allows us to observe our body’s molecular processes directly then we will not be consciously aware of telomeres altering in length and so we cannot control them directly. But we do have some control over our lifestyle and so, using willpower, if we trust in the science, we should be able to have some control over telomere length indirectly.
So their length may change due to our conscious will but we will be unaware if we have been successful.
Okay, that sounds like a much more modest version of what you said earlier. Of course, if you decide and stick to live a healthy lifestyle, that in turn has consequences for the kinds of physical and chemical reactions that take place in your body, so in that sense it is true you can “decide” to affect your body’s internal chemistry. Not eating lots of junk food can prevent heart disease for example. I would agree to that. But that is a far cry from what it sounded like you were saying earlier, that you can somehow just “will” particular physicochemical states to manifest in your body. If you eat a lot of junk food for example, you can’t just sit there and “think” or “will” the negative health consequences away.
No Rumraket, you are not getting it at all. Its not about living a healthy lifestyle. Its not about what food affects which system in your body. Or what exercise does to your chemistry (although that’s also magic).
Its about the attitude you choose, affecting the actual state of your DNA. By choosing to think a certain way, you are changing the very chemicals that supposedly cause us to think a certain way. The video is exactly about willing certain physical manifestations to take place.
There is no materialist explanation for this, nor could there be.
Here’s one: You are sort of like a computer, you have an internal architecture, and you have inputs and outputs. Given certain inputs, your architecture will process those inputs, and you will produce an output.
So you could have an architecture such that, given certain inputs, your output is to alter your architecture. Clever right?
An real world example of this is, well, your actual computer. It has a hard drive, and on this hard drive are stored instructions for how to process inputs. One of those inputs could be you typing into particular files on your hard drive, which in turn are processed by your computer. But those files contain the very instructions for how to process inputs. Thus having satisfied the condition of altering the behavior of your computer, because the inputs were processed in such a way that they altered the physical architecture of your hard drive (the magnets that correspond to the ones and zeroes encoding the instructions were altered when you wrote new code into the program).
So for you, as a biological human with a brain, it could work in a way just like the computer. Your brain functions in a certain way according to it’s architecture. it will respond to certain inputs with certain outputs.
You see some information, which we call the input (the video you watched), and the architecture of your brain is such that, given this input, internal processes will enable particular chemical reactions in your brain, thus altering your brain’s architecture, with the result that you behave a certain way (you decide to think certain thoughts).
And now you’re thinking you somehow “willed” yourself into a different chemical state. But it was just the kind of thing that your brain does, given certain inputs. One of it’s outputs is to alter it’s internal architecture, given those inputs. This in turn also causes your behavior (you sit there and feel that you are “willing” things to be a certain way).
There you go, an explanation you said could not possibly exist. The very instrument you type on with your fingers should be physically impossible according to you.
Please spend some time reading what external and internal means, and let me know when you think you understand the difference. The hard drive is not changing the hard drive by changing its hard drive.
Right now you are obviously very confused.
I didn’t say the hard drive alone is changing the hard drive. It is the computer, the totality of the hardware, which has a particular behavior, which is in part explained by what is stored on the hard drive. The hard drive is part of the architecture of the computer, which explains why your computer reacts a certain way to certain inputs.
And it is possible for an external input to alter what is written on the hard drive, in turn altering the behavior of the computer and how it responds to future inputs.
The same could be true for you. You could have some stored instructions (your chemicals in your brain) for how to react given certain inputs(they react in a certain way to external stimulus), and when you meet those inputs, you (the chemicals) react in that way, but one of the ways you (the chemicals) react is to alter your stored instructions (alter the chemicals). You call this fundamentally material interaction the “working of your will”, but it was really just chemistry.
The matter has thus been conclusively settled. Thank you, happy holidays.
Does His name start with a “W”?
Yes this is a fine display of your individuality. We don’t find prokayotes adding on purposes in this way. They’re not rebels, they stick to the rules unlike us humans 🙂
The purpose of all these molecular marvels is to work in a coordinated way to maintain the vitality and continued existence of the whole organism. And thus the whole organism will be able to produce more of its kind. This is what we observe so I’m not going to make any further speculations on how much more variety will be generated by this process. The variety that we can observe through the generations is a fair amount but it is limited.
Yes, it would probably be better to talk about function rather than purpose. In fact instead of observing and then speculating we would do better to observe and try to understand the processes in as much detail as current research allows.
If I am talking about our individuality I would hardly make distinctions according to race, as that has nothing to do with individuality. The evolution of humanity is a progression out of tribalism and race to the point that we see around us today where more and more people have the freedom to follow their own individual paths rather than following in the footsteps of their forebears or cultural dictates.
My last sentence would have conveyed my meaning better if I had said “most individuality” instead of “most differences between them”.
Can you explained how these organisms you mention display their individuality compared to species wide behaviour? If you wish, I could do the same for humans so that we can make a comparison.
So far we have understood that molecular processes in our bodies are somewhat dependent on our will. And machines, before they become actual physical entities begin as thoughts and ideas in the minds of individuals.
If you want to argue that these thoughts are themselves the products of material processes then you need to ask yourself the question: “Why would chemicals suddenly get the urge to create machines”? What induces the interaction of chemicals to come up with ideas and desires?
My apologies – I was being too subtle. My point was — you, Charlie, are being anthropocentric. All bacteria look the same to you, all cannabis plants look the same to you, because you are unaware (or indifferent) to the differences between them. So you conclude that “Humans as a group consist of individuals which have the most differences between them.” which is a really silly thing to claim.
When I added “Thank you for not extending your argument to different races, that often gets awkward.”, I was riffing on your indifference to the differences between different horses [say] by alluding to the ancient “they all look the same to me” trope. Cross-racial identification is in fact problematic, but my humor was a reductio ad absurdum : if you had claimed that “Caucasians as a group consist of individuals which have the most differences between them.” we would have all had a good giggle, right?
But your anthropocentrism is leading you astray in precisely this manner.
Cannabis and hemp; same species, displaying their individuality:
You have explained how cannabis and hemp display the physical differences of the mature plants. That is one attribute, so I will give you one human attribute and add one more. Although humans are omnivores, some humans refrain from eating animal products. And a second individualistic trait decide to have themselves sterilised which obviously prevents them from producing offspring.
Would you be willing to continue with this and make a list, as long as you want, of attributes (which are not species wide) within a species of your choice, and I will do the same for humans.
As Goethe noted after his trip to Italy, plants of the same species will have quite a different appearance depending on the environment in which they grow. It might be better to narrow the comparison to fauna, but if you want to stay with plants then that will be fine with me.
Judging this solely on how members of a species look is IMO superficial. And if you are to back up your claim that I am being anthropocentric then we will both have to look at this objectively.
So do you want to compose a list so that we can make a comparison?
Impressive. I could provide you with a hundred different yeast cells, each one has distinct nutritional requirements.
Kinda like the slime mold cells that choose not to procreate.
“Better” for your competitive cherry-picking, perhaps.
Okay, I laughed out loud at the “superficial” line. My original example (lamboid superinfection) is a matter of life and death for the bacteria and phage involved. I chose hemp/pot for the obviousness of the visual.
Your choices of criteria are hilariously anthropocentric. There are plenty of species where the phenotypic plasticity is so great that nobody had any idea they were the same species. There are some eels and barnacles that come to mind, but there is no point in making any lists for comparison: I am quite satisfied that I have demonstrated your anthropocentrism. Without even mentioning the cliche, dogs.
Until that darn atheist philosopher Thomas Nagel broke rank with Mind and Cosmos.
You have tried to match my examples of individuality in the single human species by selecting attributes from multiple species. And even then your examples do not demonstrate individual choice but acting out of necessity or having the variations forced upon them from without. And you accuse me of anthropocentrism while you talk about slime mold cells choosing not to procreate as if it were equivalent to humans choosing not to have kids.
That’s my lot for today.
Well, I am curious to know from atheists, how much evidence would be enough?
Can’t you virtually always just make the claim that its just coincidence or illusion, or hallucination or whatever you want to say? You know there actually are studies done by respected scientist that have shown positive results for esp, for children having knowledge of previous lives, for afterlife experiences, etc. But its easy for anyone to dismiss something if that is what they choose to do.
So if free will, or consciousness, or coincidences aren’t enough, then why should anything be.
Nagel’s arguments don’t have anything to do with vindicating free will, which is the topic of your tangential discussion with Rumraket. Nagel’s point is that there’s no physicalist explanation of consciousness. That’s a separate point from whether or not there’s free will.
Yes. That’s why it’s a leap of faith either way.
Some leaps are better informed than others. 🙂
But that was somewhat the point of my post on Evolution and Probability. No one knows what the probabilities are, or the priors. So belief is based on preference.
But the number of atheists who will admit that are rather limited. And when they claim they have the evidence on their side, well, that’s when they really are telling whoopers.
There’s plenty of evidence against atheism, but whilst they are leaping, most are also closing their eyes.
Free will is only a relevant discussion once we get past physicalism, isn’t that necessarily true?
Ironally, I don’t consider myself a materialist. And I’m not defending materialism in this thread because I think materialism is true. I’m really just criticizing bad arguments against materialism. Phoodoo presented his post as a huge target when he asserted that there could not ever be a materialist explanation for the phenomenon he alluded to, so I objected merely show how such an explanation could look.
To me the big question is consciousness. What explains, if anything, the qualitative contents of conscious experience? It seems to me that it isn’t possible, even in principle, of giving an account in terms of the actions of the laws of physics through interactions between atoms and molecules, or as fluctuating fields, that fully explains why it is that when I see the colour red, it appears to me the colour it does.
If materialism is the proposition that all phenomena can be explained in terms of physics, then I’m not a materialist, because I think the qualitative contents of conscious experience is a manifest counterexample to the materialist proposition.
Let’s imagine we try to give a materialist account for my experience of the colour red. What can we do here? We can give some sort of account of atoms and molecules moving around in spatiotemporal relation to each other. Molecule A reacts with B, producing complex C and so on. When in this explanation do we come to have “explained” why red appears to me like it does? It is clear that this can never actually happen.
That said, I think there are still very good reasons to think conscious experience is tied to particular physical structures, such as brains. There are so many strong indications that physical and chemical manipulations of the brain can alter conscious experience, and even shut it off completely. So whatever consciousness is, it has something to do with brains and the physics and chemistry that takes place inside them.
That seems to put us in this strange position where the emergence of conscious experiences from physical stuff is fundamentally inexplicable.
Even worse, it seems to me there can be no explanation for consciousness even in principle. Whether we discard materalism or not. What would an explanation for consciousness look like if we look elsewhere than to materalism? I still can’t even imagine one.
The supernatural has no more explanatory power here. How would a supernatural explanation for consciousness look? “A supernatural force makes conscious experience exist”. How is that any more of an explanation than “A physical structure makes conscious experience exist”? Both statements are equally vacuous, as neither of them explain how or why conscious experience comes to be, or why it is the way it is. How would supernaturalism explain why it is that red appears to me the way it does? “A supernatural force makes red appear to you the way it does”. How is that any more of an explanation than “electromagnetism and gravity makes red appear to you the way it does”? Again, both statements are equally vacuous, as no actual explanation is given. It is merely asserted that “label X makes it so that you have that experience”. What does “makes it so” mean here? How does it make it so? Where is the explanation?
This puts us in a philosophical dilemma. Are we to just accept that, that conscious experience is without any possible explanation? I have a strong intuition against that. It feels like giving up, and I want explanations for everything. And yet I can’t think of how that could be done for consciousness. That seems to make consciousness a brute fact. Something that is the case for a fundamentally inexplicable reason, if any at all. I don’t know how to grapple with that other than to say “I don’t know”.
Correct. Could that be the source of what you call “inner activity”? The striking properties of complex proteins and organisms are both the product of (adaptive) evolution.
You are positing the existence of archetypes and group souls but are unwilling to speculate how much variety is generated in populations? Tch 🙂
Agreed, purpose is often in the eye of the beholder.
That gets asked more often. Hard to tell. All I can say is that I do not see sufficient evidence now.
Shall we talk about evolutionary biology phoodoo?
Saying that God is the reason for free will, or consciousness, isn’t really a satisfactory explanation for me. It’s good that it works for you, but for me it doesn’t. Therefore, it is not really an incentive to start believing.
We’ve had that discussion (How are decisions made in phoodoo world) and you literally could not say a single thing about “free will” other then you have it.
It’s not really an explanation at all. It’s just an excuse for the lack of one.
The real question is what is the evidence for your particular deity?
After all, I doubt Thor is impressed with you currently given you are worshipping another god. But perhaps Thor is the true creator. There’s literally no way to tell is there?
Thank you Rumraket for that honest, thoughtful post.
IMO in any philosophising about this we should make sure that we begin from a point where as few assumptions as possible are made. When we say “I am conscious” we have already divided reality into entities, myself and that which I am conscious of. What justifies us in making this distinction?
Anyway, it was an interesting read 🙂
Sure there is.
Well I think the justification for that is the very experience in question. I have the experience of being myself, of being present in a particular location, of having some sort of spatial boundary, and an experience that there are other things that are not part of me but I only interact with. I don’t have an experience of being the chair I sit in, or the the coffee I drink.
I can see out my window and the trees are moving in the wind. I cannot feel that wind, I don’t think I’m the tree standing in the wind, and it isn’t part of me. I’m pretty sure I’m “just” this semi-hairy primate sitting in my chair.
I’ve been thinking about this word “source” and how it suggests a point of origin. So we get into the habit of thinking of everything as originating from a central point which radiates outwards. And this is why standard teaching always leads us to believe that everything originates from fundamental “particles” which are infinitely small. But what if things can also originate from a peripheral plane? We would then have an interplay of outwardly radiating influences and inwardly reducing wave-like influences.
When we think in this way the double nature of the quantum world does not seem so strange. All these nano-complexes we have been discussing do not just form by expansion of amino acid chains, in order to actively function they have to condense into a meaningful dynamic form. The separate scattered components have to come together to form the complex. .
You mean as in adaptation of finch beaks or peppered moth wing colouring? Adaptations like this just means that those organisms that already possess the beneficial features do better than those that lack them. It adds nothing new. This is just variation within the archetype.
The archetype is just the range that any organism within the kind in question can fall within and still remain of that kind. For instance all dogs would be within the canine type. Dogs come in a great variety of shapes, sizes and temperaments but they are all recognisable as dogs. This is due to the fact that they all conform to the archetypal dog.
And concerning group souls, if we study animals we can determine certain activities that they have in common with all of the members of their kind and which activities are individual. Instinctive behaviours would fall under group activities and therefore belong to the group as a whole, whereas learned behaviour as in the crow making a tool is individual and not common to the group.
I could substitute the word, “soul” for “personality” but then I’ll be in danger of being accused of anthropomorphism. The point is I am not just using these terms because of pure speculation. If we study and compare vertebrates we can see a progression from those in which a shared common nature are more the norm to those which display more individuality. The face is an ideal place to see this. Compare the range of expressions on the faces of fish, frogs and primates and you will see which of these shows more individuality. And if we want to look at a narrower range, we can do the same for, say, an aye-aye, a chimpanzee and a human.
Look at the general form of the face and you will see the group nature, look at the expressions and you will get more of an idea of the nature of the individual.
Hey! There are things we can agree on 🙂 It’s fun to argue but I do like to see the occasional patch of common ground.
And you accuse me of being anthropocentric! Are you not thinking about life and death from a human perspective?
Are you saying that life and death has the same meaning and consequences for bacteria and viruses as it has for higher mammals such as elephants and humans?
Thank you for these 🙂
Humans design objects and images which are representations of their own features. They are the product of human individuality. What other organisms do this? Another item which I could add to my list of human individuality.
No, there is not. You appear to be mistaken in that belief.
Why don’t you demonstrate how to determine from which of the many gods humanity has invented what is actually the true one?
It is interesting how your reactions occasionally resemble those of the creationists here. Modifications of existing structures are not new? Excuse me?
And what is “beneficial” and what does “do better” mean, if not increased survival or reproductive success? The entire thrust of living beings is procreation, yet that never shows up in your musings. Why is that?
Why would you be? Animals clearly have personality, right? Don’t you have pets? Do you have great difficulty distinguishing your cat/dog/gerbil from its compatriots? Never was a problem for me.
Sure thing 🙂
I was talking about finch beaks or peppered moth melanism, and in these cases the variations already exist in the populations, it is just the frequency that changes.
“Beneficial” and “do better” means that they are better able to survive.
The entire thrust of living beings may be centred on procreation, but this is not the case when it comes to humans. Human procreation is largely down to individual decisions with many people choosing not to participate. Even the recent situation in China involved individuals making decisions for a whole nation and this turned out to have had disastrous unforeseen consequences. And when the authorities relaxed the rules in order to allow couples to have two children, many declined to have a further child as they did not think that they could afford it:
Do you believe that animals have personality on a par with humans, that they should be considered people? Have you ever kept slow worms, stick insects, or the like as pets?
Easy. None of them.
Looks like Omgain is applying the evolution of cars fallacy again…
All he needs to prove is that the newer car models not only have designed themselves but also self-assembled…I’d suggest the quantum processes for that the same ones that self-assemble flagellums as the chemical bonds in the particles of the car parts would prove futile to accomplish such a task…;-)