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 …
All thermodynamics is local. 🙂
You appear to be struggling with the word “fundamental” 😉
If by ‘fundamental’ you mean what current, best fundamental physics says, then the answer is everything is made of the fields in quantum field theory.
That’s as far as you can go with science. If you want to talk about whether quantum fields are “material” and whether “less fundamental stuff” is “made of” such fields in some sense, then you need to get into philosophy (hence the scare quotes).
Start with your preferred QM interpretation and proceed via scientific realism (or not) through reductionism to metaphysics.
If you want to include God, make a side trip into philosophy of religion and possibly your favorite theology.
BruceS,
Jonas definitely had vitalistic tendencies, but I tend to read those as unfortunate contingencies of his thought rather than anything essential to it. If he had known how close we are to embedding our study of autopoietic systems within far-from-equilibrium thermodynamics, he might very well have rejected his own tendencies towards vitalism.
But what Jonas is definitely right about in The Phenomenon of Life is that organisms display an intrinsic purposiveness as a result of their “needful freedom” vis a vis their environments — organisms both stand apart from their environments and essentially depend on them. Jonas develops a rather nice phenomenology of life and uses that as a basis for criticizing Heidegger.
In any event, I only mentioned Jonas here because he develops a nice philosophy of organisms that focuses on how organisms are distinct from machines by virtue of their intrinsic purposiveness.
But I do not think there is anything in Jonas that contradicts Darwin, or vice-versa.
I think that the idea that organisms are machines can be blamed on the French.
I don’t know if you were intending to be facetious but that’s actually true. It was French materialists like La Mettrie and d’Holbach who really tried to apply mechanistic materialism to organisms. Jonathan Israel claims they were influenced by Spinoza but I don’t have the expertise to evaluate that interpretation.
Rumraket argues that every organ that comes into existence is by definition fully formed. So I guess all of our organs are both fully formed and undergoing trial and error. This is the absurdity of evolution.
They can never ever, point to a present day example of novelty coming to be, because everything seems to be fully formed and changing into something else. Of course then shouldn’t there be packs of wolves with some possessing a sonar like device for finding buried food and some without, caught in a snapshot of time before the ones without sonar will eventually all be out-competed?
Evolutionists ask you to ignore what they say happened in the past, don’t ask to ever see it happening. Evolution stopped, a few hundred millions years ago (but don’t worry because that is like yesterday evolutionary speaking.)
Not entirely facetious. There’s usually some kernel in what I write that can be found for those who care to investigate further. I am reading the book Evolutionary Theory and the Creation Controversy. It’s quite interesting.
This in a section on organisms and the universe seen as clockwork and machine where the organisim is seen as “the microcosm that mirrors the macrocosm.”
Does Rieppel give specific names for the French biologists he had in mind here? I ask because d’Holbach and La Mettrie (the French materialists I’d mentioned above) were definitely not “well aligned with religion and politics, with the ideals of people with wealth and power”. Maybe le Buffon or Cuvier?
I’m not quite sure how he made that connection. It’s in a section on Charles Bonnet, who was Swiss, and Albrecht von Haller, also Swiss.
I was going to blame it on the Swiss. 😉
What is the absurdity? Being fully formed doesn’t mean being perfect, or capable of anything and everything. Presumably your arms are fully formed, but are you a world champion arm wrestler? Turns out your fully formed arms can still improve in a multitude of ways. You can train them so they get better at something, or evolution can happen and the arms of our species could in principle adapt to environmental challenges that they aren’t currently as capable of.
No absurdity.
You have never defined what you mean by “new” or “novelty”, so I did it for you, and it immediately followed from the definition I used that you were wrong.
You don’t like my definition? Then come up with a better one, and… actually just come up with one for starters and we can proceed from there. Define your terms.
No, why should there? How does that follow?
Where do I meet these evolutionists who ask you to ignore what they say happened in the past? Quote them making that statement so I can join you in repudiating them.
Ahh see this is confused, because there’s a difference between asking “what happened in the past?” and “can I go back and see it again?”. None of us were around to see the Mt Everest form, yet we know that it did, and in broad strokes how. It is no different with evolution. We make inferences about the past from observations of present phenomena, and our understanding of the forces of nature. We can’t time travel and replay the events before our own eyes, satsifying as that might be. But if that is your criterion for accepting historical claims, you are consigned to remain forever unconvinced of anything you didn’t see happen yourself.
Who says evolution has stopped? From what does that follow?
Eyes are easy to evolve, remember? So we ought to see new eyes appearing all the time. Right?
Evolutionists don’t even believe their own propaganda, so why should I?
Why does that follow?
What propaganda? This general commentary of yours is infantile.
Is not.
Have you forgotten already your own argument? The more frequently we observe an event the more probable that event becomes. So wouldn’t it be the case that the less frequently we observe an event the less probably that event becomes?
When is the last time you observed an eye evolving from something that was not an eye? Now extrapolate that to other features like the brain. Or lungs. Or wings. Or whatever.
When’s the last time you saw the genetic code evolve? Or an additional nucleotide added to DNA. Or an additional amino acid added to proteins.
It certainly appears to any objective observer that evolution has ceased.
And yet homo sapiens have only been around for a few hundred thousand years, did you somehow forget about the pinnacle of evolution?
Must be hard to evolve an homo sapiens then.
Hard? you mean impossible, right? because evolution stopped when the last new organ evolved.
No, I don’t mean impossible. Just very very improbable, as evidenced by the fact that homo sapiens has only appeared once, in all the history of evolution. Unlike the eye.
How is it not impossible if evolution has ceased?
What is so difficult to grasp about the logic?
If there are lots of eyes, eyes must be easy to evolve.
If there is only one homo sapiens, homo sapiens must be difficult to evolve.
Miraculous, even.
It would be miraculous if you actually cared to address my actual point, but you can’t expect miracles from creotards.
Uh, wow. There is only one of every distinct species, but there are millions of species. So should we conclude that species are easy to evolve (there are so many), or difficult to evolve (because there’s only one of each)? Or do we conclude that the miraculous evolves easily?
Underlying all this is the forgotten notion of Deep Time. Even during the eyeblink geological period people can examine with any confidence, a very large number of species has evolved. Problem is, single branching events produce “new species” so similar only members of those species can tell the difference, and even they seem to have difficulty doing so, and there’s significant but diminishing interbreeding during many branching events, which might require millions of years before all gene flow between the emerging species and the “parent” species has stopped.
Current evidence, by my reading anyway, is that as our species emerged, there may have been as many as half a dozen concurrent species of hominins. All but ours went extinct, and ours went through at least one bottleneck even where very few survived. I’d say the number of possible species is so nearly infinite that the probability of any particular one of them is near zero, while the probability of a great many is clearly very high. And geologically speaking, the lifespan of most distinct species is short.
That’s right. We are not miracle workers. We leave that up to people like Dawkins.
Yes. Generally speaking, the frequency with which you observe the outcome is the probability that outcome will occur on that event. How often do you see, on average, the outcome “6” face on the event “roll a six-sided die”? Probably about 1 in 6 times. So the probability of that outcome is 1 in 6, or ~0.167
But rolling dice and watching evolution are very different things. Evolution of the kind you refer to takes geological time. That doesn’t mean evolution has stopped. It’s just that the kinds of transformations you would like to see take much much longer to occur than a single human lifetime. That problem isn’t unique to biology. When was the last time you saw an island erode? Or a mountain form? Or a continent? Or a galaxy?
We still see evolution happening, we just can’t stick around to see it on the kinds of timescales it took to form things like eyes and organs. The fact that you have not personally witnessed eyes evolve doesn’t mean evolution has stopped, or that the probability of eyes evolving is zero. It simply doesn’t follow.
The fact that an outcome (eyes) has occurred independently something like 50 times (say) over the course of the history of life (roughly 4 billion years), doesn’t in any way imply it should be observable to happen in a human lifetime. Particularly considering every instance of the process from the origin of light detection to recognizable morphological eyes, is implied by the evidence to have taken tens to hundreds of millions of years.
And this all ignores the things countless things we have seen evolve, which of course all completely disproves the frankly idiotic claim that evolution has stopped. I don’t see eyes come into existence so oh gee that must mean nothing at all evolves in any way anywhere.
C’mon.
What about them? There are things we can directly observe take place, and things we can’t which instead we are consigned to infer take place either by extrapolation of directly observed processes, or infer took place in the past from particular patterns in the data we have collected.
Depends on whether you mean “change” or “originate”. I have not seen the genetic code originate (and that very well could have happened only once), but there are observed instances of evolutionary change to the code. As in mutations that cause changes to the genetic code in certain species
But supposing the genetic code only originated once, does that entail that evolution has stoopped? Of course not. The fact that it only came into existence once does not mean it has stopped changing, nor does it mean that everything else has stopped evolving too.
It just doesn’t follow.
Your entire argument is ridiculous. It is invalid reasoning and plainly, obviously false on it’s face.
I haven’t. Does it follow that evolution has stopped? Nope. The claim that evolution continues and hasn’t stopped is not contingent on a requirement that we observe new nucleotides being added to DNA. Obviously. Obviously.
Uhhh, an amino acid insertion in a protein? I’m sure that has been observed hundreds, if not thousands of times.
Or did you mean a new amino acid added to the genetic code? That has also been observed in artificial selection experiments. Strains of cells known to have promiscuous translation system enzymes were subjected to selection in an environment containing noncanonical amino acids and eventually yielded strains with an expanded genetic code.
Are you seriously making Ken Ham’s fatuous “were you there” argument? Must we see it happen ourselves, or we can say nothing about it? Come on Mung.
Your so-called “objective observer” seems to have forgotten that none of the entities listed are thought to have evolved in a human lifetime. The conclusion that evolution has stopped cannot be valid when it is based on a demand to see processes complete on timescales incredibly shorter than those in which they occur. Nor does it follow that evolution has stopped even if there are instances of particular structures or entities that no longer originate or change very slowly.
Dawkins is a miracle worker?
Yes. He’s managed to convince otherwise reasonable people to abandon reason and join him in a magical adventure where imagination trumps reality.
But where oh where are the packs of wolves (or sheep, or aardvark…) where half the population have a majestic new organ, and half don’t? And the other half are on the verge of becoming obsolete because the organ confers such advantage?
If this is how EVERYTHING came to be, why has it stopped? Ok, fine it hasn’t stopped, we will see this one day, somewhere, anywhere, but its so exceedingly rare, that nowhere on the planet does this scenario exist…but just wait.
As a self-admitted theistic evolutionist you too are in that magical adventure.
Why half?
Obsolete? What a strange word to choose.
If your god made everything in a week, why did it stop?
It’s not rare. All species are transitional species. That you don’t understand what you pretend to criticize is a lack in you solely.
OK, thanks for the feedback. I have not studied him beyond the web page you linked, so it would be unfair for me to go further with my concerns.
I do think that “Dynamics in Action” has an interesting take on purpose/teleology in organisms. I’m not saying it’s correct, only that it shows one way to build on ideas in dynamics and information without introducing anything like vitalism.
I also like Godfrey-Smith take on synthesizing these types of ideas into a unified approach to life, cognition, subjectivity, phenomenality.
Mind, Matter, and Metabolism
OMagain,
Because at some point, if a mutation is creating something novel, something that makes others without the mutation less fit, then eventually we got to get to half, before we get to the whole population acquiring that new organ.
But if half is asking too much, how about 30%?
How about an individual?
And it seems to be your claim that an individual can have a single mutation that causes a brand new organ to be present? Is that correct? That a single mutation has the power to generate a new organ in a single step? Am I understanding you correctly?
OMagain,
Well, I am not sure what a partial organ to use sonar to find underground food looks like, but I suppose its something like a partial nose. We gotta start somewhere. Any partial noses in half a population? 30%? 24%?
This is how EVERYTHING came to be after all, remember? Sure is fucking rare.
What use is half a wing? What use is an eye that can only detect dark/light?
What’s a partial nose? What’s a “nose”? How many different types of “nose” are there? Do you assume that your human nose is the only possible way to determine what chemicals are in the air?
You don’t get to say “we”. You are not part of that grouping.
Simple question: Do insects have noses?
How do you know a nose is a partial nose without the ability to look into the future?
Nose size seems to be related to the temperature of the nose owner. Before we moved to colder climates, was the nose incomplete as it was not what it would be after that time?
https://www.smithsonianmag.com/science-nature/how-climate-changed-shape-your-nose-180962567/
So you’ve actually picked a great example. The nose has adapted due to the niche we’ve found ourselves in.
So, which nose is the 100% complete nose phoodoo? The warm air nose or the cold air nose?
How about the no nose, and the nose that only half the population has, because there hasn’t been enough time yet for them to completely out-compete the noseless?
You know, from nothing comes something. You seem to struggle with a pretty easy concept. I wonder why you believe in evolution.
We can observe the difference between living tissue and dead tissue. Living tissue either has vitality and activity or it has the potential for vitality and activity. What happens in your PCR is a living process. They even talk of the polymerase used in PCR processes as having a half-life.
There is no vitalism required, if by vitalism you mean some external life-force hovering over the substance. The life-force belongs to the polymerase itself and is as much a feature of it as the physical matter of which it is composed. It only becomes dead substance when it loses the ability to have inner activity.
On a glass slide, both bacteria and Taq polymerase are living as long as they are showing signs of activity. Some things have the ability to retain the life-force more than others. Plant seeds have more of this ability than petals. Likewise our liver tissue has more than our brain tissue. A rose in a vase has more than a dried rose and this can be observed easily.
The biochemical experiments you are talking about would not work if they did not use living substance.
The lack of self-replication does not preclude them from being living substance.
Anyone who just sees it all as physics and chemistry will deny this essential difference between living and dead substance and so will not even bother to undertake any further research into the difference. IMO this is a missed opportunity.
And the moral of the story: The purpose of adverts is to attract the gullible. Is it too late to get your money back 🙂
My thoughts on seeing evolution in action:
Comparing evolution to individual development is like comparing the hour hand to the second hand of a clock. We can see quite easily the movement of the second hand. The hour hand is also moving but it happens too slowly for us to observe it directly.
Want some dressing with that word salad?
If you’d like to rephrase that in an intelligble way then perhaps it can be responded to.
I don’t believe in it. I accept that it is the best supported explanation for biology. If you give me a better supported explanation I’ll accept that in turn.
I don’t have to believe in things which there is demonstrable evidence for. Belief is simply not required. You think that everybody thinks like you do. They don’t.
And from nothing comes something is in fact your position. One day there was nothing then another day there was Adam, fully formed. Given that’s literally what you believe it’s ironic what you are saying here.
But I guess introspection has never been one of your strong points. Or you’d be able to say how decisions are made in phoodoo world, right?
How does Intelligent Design Creationism explain the observed changes in nose shape in relation to the temperature of the environment?
If you can’t say, why do you believe in Intelligent Design Creationism?
You seem to have this view of evolution where suddenly an individual is born with a mutation resulting in an entirely new organ, like a liver, and nobody else in the population has any inkling of a similar structure, and then this new organ mutation must rise to fixation in the population. That’s ridiculous.
Where has he done this? That sounds crazy.
The proportion of the population with novel mutations isn’t the issue, it’s that you think the mutation must result in a completely novel organ, rather than gradually evolve an organ from an existing structure.
You are skirting away from the fact that your theory proposes that not only do changes provide a continued positive effect on the ability of that organism to have offspring compared to the rest of the population without the mutation, but that also the change has to start somewhere.
So a nose starts somewhere, a lung starts somewhere, a kidney starts somewhere. And in the process, that something that starts it, has to slowly spread throughout the population. And as bruce as pointed it, first the mutation must spread to all individuals, THEN, the next mutation can happen to piggyback on top of the first one and make it better.
So it follows, there must constantly be populations which have some members with the new mutation, and some without. But that situation is pretty dam hard to find in real life. In fact dam near impossible one might say. You can go and claim, “oh well, some people have stronger arms then others, so see, that’s an example.” But if that was the case, if that was the beginning of a new use for arms, then we should see the cases where there is an actual NEW use of arms, and not just various shapes of arms, all still just being arms.
There needs to be a whole spectrum of progress, from the first mutation, to ones that are slowly spreading, to new uses of organs. And there must be a lot of these, because evolution must be continuing all the time.
And yet, not.
If you can’t get that, much like Omagain can’t, that’s not my fault.
At what point does it cross over from not-nose, to nose? How different must the anatomical features be? How big must the structure be before it is a “nose” rather than a flat surface with an opening?
It is not at all obvious you would even be able to recognize the beginnings of the kinds anatomical of changes you want to see. What we can show you in real populations is something like the difference between two consecutive letters in my terrible drawing here, like A-B, or G-H. But you seem to want to see a population where 70% of individuals are like A, and 30% are like P. That’s not how it works.
Oh crap.
Any process where the rate of reaction (e.g. decay) is proportional to the amount of substance unreacted will exhibit a so-called exponential decay. Radioactive decay is the most well-known example, but enzyme denaturation can also show this pattern. An intuitive way of describing the RATE of decay is to quote the “half-life”, that is the amount of time it takes for half of the substance to decay.
After two “half-lifes” only a quarter remains, after three, an eighth, etc.
It’s got NOTHING to do with having any vital essence.
And there is. Everywhere around you. But the differences between mutants are often times almost imperceptible. There is a real distribution in the physiological characteristics of all natural populations. Some are shaped ever so slightly differently than everything else. And they often follow a gaussian, so the more extreme the difference is from the mean, the more rare it is. Have you ever wondered what explains this distribution?
What is new? Define new. At what point does the usage of arms become new? Would you recognize the changes?
At what pixel does this cross over from red to blue?