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 …
Odd how no IDC ever considers the onus to be on them to show their claims are true.
I guess that’s why IDC has been so wildly successful in replacing “Darwinism”.
There exists only ONE definition of the word “machine”? I find that a little hard to believe. 🙂
That word and “apparatus” signal to me that the definition was created with man-made machines in mind. Not entirely apropriate to describe cells or organisms that way, I think.
Why would I need to show that some machines are not constructed, when THE definition doesn’t call for that?
Corneel,
Why do you keep wanting to distort defintions?
How does “apparatus’ mean it can’t be living?
ALL THREE of those examples can apply to living things. A clean sweep!
You want to call soft cuddly bunnies machines and it is ME that distorts definitions?
“a combination of instruments, machinery, tools, materials”
Yep, that sounds just like a living organism.
But my main point seems to elude you, so let me repeat it: If you somehow get organisms to fit the definition of machines, you can no longer cash in on the fact that all known machines are constructed. So this entire semantic exercise seems rather pointless.
DNA_Jock,
I think It’s more that he believes in a scala naturae, with us (or chimps, I’m gonna keep making that joke!) as its ultimate goal.
Thanks for the link.
I think that the machine metaphor has become popular because we humans like to see things from our subjective perspective. The same way that we see faces in the landscape or the clouds. We have moved on from the days of the industrial revolution with all of the mechanical inventions where nature was seen as clockwork, to the present electronic, information age where nature is seen in a similar light.
The benefit of this progress is that the dynamic, fluid aspect of molecular life is now beginning to be revealed, and so instead of viewing life as compared to human inventions, we are finding the vast amount of marvelous processes and structures that can be copied from nature. The composition of life has infinitely more to it than we could ever imagine.
And we can try to mimic what if found there without the need to define what is or is not life.
Have you read any of the literature or watched any videos on intracellular activity?
Could you give an example or two of functioning protein complexes existing outside so we can discuss it ?
Nowadays it’s the “information” metaphor.
You mean as in finch beaks or peppered moths?
CharlieM,
Are you arguing against yourself here? You didn’t strike me as a species immutablist.
No I don’t.
I have nothing against anyone who speculates that their migration abilities have a genetic cause. This is no different to me speculating that group memory is involved. But if you want to tell me that it is more than just speculation then you will have to give me more details on the relevant genes.
Haha. So for any trait for which gene names can’t be provided, you invoke any old crap? Because without detail, any answer is as good as any other?
I wonder what is the reason for the odd behaviour of juvenile birds in displacement experiments? The group signal’s a bit weak? Nothing to do with innate triggers?
Genes are a known causal agent, and for many traits, we do know the genes. So, in a hypothetical, we say “X is caused by genes”, and you say “tell me which genes or I say it’s … wibble”. So we respond, “actually, in this case, it is caused by genX”. What do you say then? “OK, I stand corrected, X isn’t caused by … wibble … after all. Now, about Y …”.
I think you might need to actually demonstrate the existence of wibble. This is not shown by pointing to a phenomenon and saying “wibble”.
Yes, I would say that regarding cells, this is closer to reality.
And as for individual entities such as bacterial flagella systems, if we want to compare them to human designed outboard motors, I’d say that outboard motors can be compared to one aspect of flagella and that is that they both convert energy in order to achieve propulsion. But we can see in the development of the human system, a progression of design improvements through trial and error. There is evidence of wisdom gained through experience. We do not see this in the flagellar system. We do not see this increase in wisdom over time, the wisdom is forever present.
That is why I wrote:
🙂
They are not machines because they are soft? Now you are getting bizarre.
Living things aren’t made of materials?
You seem to be all over the map.
Why? How do you know organisms aren’t constructed? Because you say so?
Just asking questions again phoodoo?
You can even watch the construction of some organisms on You Tube.
I knew you could watch that on youporn, but I didn’t know it was also on youtube.
CharlieM,
Like, uh, were you there? This is like wandering into a shop, examining the SpeediProp 5000 and intoning: “The perfection of this machine indicates that no trial and error process preceded it. Verily, its designer is Wise”.
CharlieM,
Indeed. I’ll say this for argument from analogy, it tries to keep abreast of the times.
What about the “information-processing machine” metaphor?
The the answer to the nature of the living cell was provided by Lost in Space (original version).
For someone who gets so upset over the use of colloquial terms to describe biological concepts, you sure are easy going about stretching the colloquial meaning of “machine”.
Everything is made of materials. By ignoring the “instruments, machinery, and tools” part, you are making your definition more and more generic in order to function as an umbrella term for your [contrivances + organisms] group. Yet nobody has any problem telling the two apart. This is why we have different words for machines and animals.
And we have come full circle again. No, organisms cannot be said to be not-constructed because Corneel-says-so, as we cannot conclude that they are constructed because phoodoo-thinks-they-look-clearly-designed. We need plausible arguments to argue one way or the other. The fact that populations of organisms are capable of adaptive change through time (evolution) is a powerful argument to explain the fact that they have a “systematic organization of activities, functions, processes, etc., directed toward a specific goal”. That goal being sustained transmission of heritable information. Calling organisms “machines” is not going to change that.
Heh heh, it evolves.
Machine have machinery. Ok, a cell is a machine, so it must have machinery. What makes you think it doesn’t also have tools and instruments?
I don’t find a single one of your attempts to describe living things as not machines as being the least bit convincing, and you have shown no evidence whatsoever to show that they aren’t compatible with the definition. In fact you have done quite the opposite. You are trying to find ONE word that machines possess that living things don’t and thus you will say see, they don’t possess….blank..so they can’t be a machine. Even though the definition doesn’t say it must possess EVERY ONE of those features to be a machine, it simply lists some features of machines.
And even with that ridiculous attempt to exclude living things, you can’t even find the ONE word you think would make it an exception.
It would be like looking up the definition of music
And then saying, oh that song does not contain ideas, it is not music. It has no color, its not music.
But worse for you, you can’t even find the ONE word to save you.
I’m not, even though the term species is a fuzzy concept.
You were saying that population change is essentially irreversible. I just think that this statement needs to be qualified because it’s not the case in Galapogas finch beaks or peppered moth melanism. these are examples of oscillation within limits and not of irreversible change.
I think I can answer that question with a resounding YES. There are machine-like terms for sure (coding, machinery), but also anthropomorphic descriptions (transcribe, translate).
A lot of labwork relies on functioning proteins in vitro (= in a test tube). The most famous one is Taq polymerase that is routinely used for DNA amplification by means of Polymerase Chain Reaction (PCR). Protein complexes is a bit more tricky, but shall I tell you something funny? You yourself already linked to an in vitro study of kinesin and dynein function. 🙂
Man, I listen to House. I am open to everything.
How about “man-made”?
But that is besides the point. Though all the definitions that you managed to find were clearly written for man-made machines, I am not denying that you could eventually come up with some generic definition that can accommodate organisms. Just as I can easily find a definition of machines that excludes organisms and vice versa.
But nothing is gained by doing that. You still need to demonstrate that the first organism-machines were constructed and that extant lifeform-machines did not evolve from more primitive precursors. Because life is so unlike man-made machines.
So we do not have to have been there to figure out the evolutionary path of the vertebrate eye but we do need to have been there to figure out that of the bacterial flagellum?
I can’t find any info on the SpeediProp 5000, so without knowing what it is I cannot say how I would react. By studying an object designed by humans, it is quite often possible to see some of the thinking of the designer.
Hahaha…it didn’t take eventually! It worked on the first try.
The challenge is finding a definition that DOESN’T accommodate organisms.
Corneel,
But you have made me reconsider one point. House is definitely not music. :>
CharlieM,
That’s why I said ‘essentially’. I could have probably picked a better word, but … you know that ‘charitable reading’ thing? If you read me as saying there is no circumstance, ever, in which a change in a population could possibly be reversed, allow me to distance myself from that position.
The same, indeed, goes for entropy change, which is why there is an arrow of time – it is essentially irreversible, even though a pedant might point to the statistical element meaning that local reversal is, indeed, briefly possible.
CharlieM,
No. I was making ironic reference to a familiar Creationist refrain. You assert, without evidence, that the flagellum did not go through a period of trial and error. But you weren’t, in fact, there, so you don’t actually know. Whereas (because you happen to know, because you were around at the time), the outboard motor did.
That, too, was a mild joke. No such make. You didn’t seriously try and Google it to see what your reaction would have been, did you? 😀
I can’t tell if you have spectacularly missed the point, or are just yanking my chain.
phoodoo,
We should not forget that there are vast differences between machines and organisms.
Stephen Talbott from the piece, Of Machines, Organisms, and Agency
Organisms may have machine-like attributes but they are not machines.
Hey! No backpedaling 😀
Allan Miller,
He was not yanking your chain.
There’s been a helluva lot of wooshing around here lately.
I am waiting for phoodoo to lay out his argumentum ad dictionarium as a syllogism. Should be fun.
I was going to respond on your behalf, Corneel, citing PCR. Heh.
You want “protein complexes”: how about in vitro translation?
CharlieM,
How many quantum biologists do you know, other than some who have to pretend to be ones to get paid?
I think Talbott is pretty much right about the ontology of organisms — that is, what kind of beings organisms are.
I had asked if you agreed that functioning protein complexes are living tissue. And you replied that they can exist outside of this context, so I asked for examples. I did not deny that protein complexes can be removed from living systems so I don’t see why you consider my link to be funny. In fact I had also linked to a video where Ron Vale showed microtubules moving on a glass slide, here.
What is the difference between putting bacteria on a slide to observe their behaviour and putting kinesin complexes on a slide to observe their behaviour? These experiments only emphasise me point that kinesin complexes have much in common with more complex individual organisms. Remove them from their natural environment but provide them with sustenance and they will continue to act in the living way that is their nature. Humans have always manipulated the living world in this way.
We take in food from our environment and convert it to provide mechanical energy for movement, kinesins take in ATP from their environment to provide the energy for movement. As above,so below.
There is a fair bit of agreement between us as to the direction evolution takes. In the case of finch beaks and peppered moths we see small changes which can be described as circular. Cyclic variation which returns to previous conditions. Larger scale evolution is more of a spiral form than circular. Cetaceans, for example, have returned to a fish like form and aquatic environment but they have moved forward and are obviously mammals. So although fish like, they will never become fish again.
This is why, if anyone argues that peppered moths are an example of micro-evolution which is just the same as macro-evolution only on a smaller scale, then I would disagree. There is an obvious and important difference here between this so-called micro-evolution and macro-evolution.
It’s hard for me to tell the serious posts from the ironic ones at times, but assuming this one is meant seriously, I’d say your continental philosophy background is showing.
Only it’s not without evidence. Can you give me any examples from the multitude of organisms of the present day where an organ of structure is undergoing trial and error? Creatures with light sensitive spots do not have them “to see if they will work”, they have them because they work in a suitable way for that particular organism.
I suspected that you had made it up and Google confirmed it. I do not want to take anything for granted. The point is that we do have the ability to study living systems and human made inventions, and the difference between them is immense and it is obvious.
More examples of humans manipulating living systems. Where once we used to only be able to work at the macroscopic level, technology now allows us to work at ever increasing microscopic levels. But it remains the manipulation of the natural world.
I don’t know any personally.
We agree 🙂 I like these words of Talbott’s from your link:
You are funny! If functioning protein complexes are truly living tissue, like you have argued in this thread, then what are we to call the experimental setup in the study? Is that living tissue? An organism perhaps? No, it is just a biochemical experimental set up. The fact that we can isolate the action of biomolecules from living system in this way demonstrates that organic molecules have no distinct properties from anorganic chemistry. That realisation was what killed vitalism in its various incarnations. That is why your arguments don’t impress anybody here.
I told you. Bacteria will multiply, kinesin molecules will not. Novel kinesin proteins need to be generated by ribosomes by translation of the corresponding messenger RNA.
I just ordered one from Amazon. According to the product description, nothing is better for cleaning your dishes, increasing your ab size, and getting a higher libido.
It was meant seriously, and yes, this does show my background in Continental philosophy — especially in Merleau-Ponty and Hans Jonas.
I only read a bit of web site, and it seems to be bordering on vitalism….
I have no problems with a different approaches to agency and subjectivity in philosophy, but the portions alluding to new kinds of evolutionary science are reminiscent of Wolfram and, IMHO, likely to have as much impact.
That is why I say God is not a thing.
But why not say that every material thing is made of materials? But what about the fundamental particles? What materials are they made of?