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 …
My views have not changed. And of course proteins are chemical substances. Their chemical makeup can be precisely determined. Of course there is more to them than just chemical makeup, for example chirality.
Not sure why that would qualify it as a living substance. We consume salt, does that qualify it as a living substance?
Having inner activity means that it is able to ingest, convert and reuse energy in order to carry out a function such as movement or growth.
I asked for opinions on the comparison of dynein complexes with worker ants carrying cargoes along a track. What is your opinion?
I linked to videos showing the activities of specific protein complexes. What is mysterious about this? Maybe you do not believe that animals move, or bacteria move, of dynein complexes move through inner activity.
I have nothing against the idea of “inner activity” but I think of it as non-linear or circular causality. That means we need to think in terms of organization or structure rather than in terms of stuff. I don’t see how appealing to machine metaphors will help us do that, though there are some important insights from cybernetics that are relevant.
It’s not just that they are organized differently, it’s why they are organized the way they are.
What is the reason that an atom is organized the way it is?
Does urea tautomerize in order to perform some function?
The human use of urea as a catalyst is more of a passive affair on the part of urea.
In what way is urea an active participant here? It is being acted upon.
Crystals have growth in common with life. Below is an image of frost growth patterns on my wife’s car.
CharlieM,
Yes.
I’m visualizing goal-posts cantering across a soccer field.
It’s a fun visual.
At this point we’re touching on two closely related and delicate topics: the concept of a law of nature and the principle of sufficient reason.
The instinctive response to “why are atoms organized as they are?” is to say “because of the laws of quantum mechanics” or something like that. That is, atoms are as they are because protons, neutrons, and electrons are as they are. But I think the question that one might ask here is, “why are the atomic orbitals as they are?” since it is the shape of the probability distribution of the electron that determines the kinds of interactions atoms of that kind can have with other atoms.
I don’t know the vast literature on laws of nature amongst philosophers of science, though I do know that at least one philosopher, Nancy Cartwright, has argued in favor of anti-realism about laws but realism about causal powers.
The trickier philosophical issue is the principle of sufficient reason, which says (depending on how you read it) that there’s an explanation for every fact. There are couple of different ways of interpreting this claim, and in my experience, when arguing with philosophically sophisticated theists it always comes down to this: is the PSR a claim about the structure of reality independent of us, or is it a claim about how we should go about conducting inquiry?
And I suspect that there are many here who expect life to be simple.
It’s not!
Again, we are in agreement. The systems of cause and effect of classical physics works perfectly well for the mechanics of human constructions and machines. But living systems are far too fluid, interdependent and convoluted to be governed by the laws of cause and effect.
And the discoveries of quantum physics are also pointing to fact that the cause and effect laws of classical physics are not universal.
Gee, what a satisfying answer. But let me help you edit it down for clarity if I may.
“Don’t ask. No idea.”
I don’t normally use the term “living substance”, so don’t ask me what I think it means. Use cell, cytoplasm, protein, tissue. More precise = more clear = better.
How does a protein “ingest” energy? As for the rest of your definition: this is starting to edge close to standard chemistry, which does not posit distinct properties for molecules in living organisms. *
I think there were two issues. The first was whether dynein motor proteins could be said to be living beings. I said they could not because they lacked certain characteristics, specifically reproduction.
Then the discussion shifted to the question whether proteins like Taq polymerase could be said to be living tissue when they were outside the context of a living entity. I argued that this is not the case, because there is nothing in the chemistry of biomolecules that distinguishes them from inorganic molecules. You objected, alluding to some mysterious “inner activity”, but have been IMO unable to define it in a way that would truly distinguish proteins like Taq polymerase from other molecules. To confuse matters, you called table salt halfway alive, because of its ability to form crystals, which recruits a decent chunk of chemical substances (except ironically, many organic molecules) into the realm of living substance.
That is where we are now. Unless you are able to flesh out this inner activity of living substance, I fail to see what we gain from calling individual proteins living beings or living substance.
ETA: * I might make an exception for the “function” part, if you drop the idea that crystallization is a function. Polymerase function has clearly evolved by virtue of its adaptive value in organisms.
Because otherwise they would be dead?
That’s not just easy humor, it’s also a one sentence summary of a scientific theory that gets discussed from time to time at TSZ (eg if one interprets ‘living organisms” are species or populations with a specific trait).
ETA: To make that last bit clearer, “dead” in my first sentence should be generalized to include “never born at all. “
If the theists know some cosmology, they are also likely to take a detour into Fine Tuning.
It isn’t me who is moving any goalposts, it is you who is beginning to have an inkling of understanding my position. You imagine the goalposts moving when all the time it is you who is moving. Your viewpoint has shifted, it’s all relative.
Nice summary, Corneel.
I’ve had a pretty good ‘inkling’ of Charlie’s position since 1979; even biologists have been known to ascribe some sort of magical vitalism to enzymes. For instance, the lecturer who introduced us to the Haldane relationship (between Km and kcat for the forward and reverse reactions) described it as something that enzymes somehow ‘achieved’. Likewise, biologists often describe enzymes as magically “using” ATP hydrolysis to achieve otherwise unfavorable reactions.
This is, of course, rubbish, and it is up to biochemists [pauses, polishes tiara] to set them straight.
[General Tip for IDists: scientists sometimes step outside of their areas of expertise; when they do, they sometimes spout rubbish. Tornado in a junkyard…]
See “List of Steves” for example.
So do you think it is possible to tell the difference between living cells, cytoplasm, proteins or tissues and dead cells, cytoplasm, proteins or tissues?
Proteins “ingest” energy by taking in molecules such as ATP. to hydrolyse, just as we take in and break down food.
Does it matter whether we call dynein complexes machines or living beings? Precise definitions are less important than the concept that people attach to the words, especially young students. Most would associate machines with human constructed devices, whereas they would associate living beings with natural creatures that live and grow and die.
I think that “living being” is a term which gives them a better idea that these structures have the properties of living substance. If we can use the “machine” metaphor why can’t we also use the “living being” metaphor if we wish? There seems to be an illogical (IMO) antagonism towards this way of thinking.
I have to go as I’m off to watch my granddaughter being a star in a nativity play, so I’ll continue this later.
My issue with the way theists use the PSR is that if they had been using it consistently, then science would have stopped long before where we are today. There is no concievable observation we could not imagine came out like it did because of “the will of God”. Why does it rain? God wills it. Why did my dog get sick and die? God willed it. Why are the laws of nature like they are? God willed it.
If the PSR means that we stop investigating when we merely have, conceptually, a “sufficient reason” capable of accounting for that to be explained, then the PSR would stop any investigation right out the gate.
Good point phoodoo,
Steven Gollmer has a Ph.D. in Atmospheric Science
Steve Overell has a Ph.D. in Solid State Physics
Stephen Lloyd has a Ph.D. in Materials Science
Stephen C. Tentarelli and Stephen A. Batzer have Ph.D.’s in Mechanical Engineering
Stephen J. Cheesman has a Ph.D. in Geophysics
Stephen Crouse is a Professor of Kinesiology
Stephen C. Knowles has a Ph.D. in Marine Science
Stephen C. Meyer has a Ph.D. in Philosophy of Science
Or were you thinking of a different List of Steves? The one with over 700 biologists on it, perhaps?
🙂
Cells and tissue (by virtue of being composed of cells): yes
Cytoplasm and proteins: no
No, they don’t. That’s just you anthropomorphizing again.
As stated previously, I don’t mind either type of metaphor, as long as young students (and certain TSZ residents) realize that proteins are neither machines nor living beings.
That sounds like fun. Off you go 🙂
ok, that atoms. Should we be asking how to account for the adaptations present in atoms?
Why can’t we just say of organisms that they are what they are because their “parts” are what they are and because of how those “parts” interact because of what they (their parts) are.“because of the laws of quantum mechanics” or something like that.
There is, presumably, something quite different about organisms that leads people to try to explain them quite differently.
It’s not just that they are organized differently, it’s why they are organized the way they are.
Are you trying to ask about why some say that they seem to be designed?
If so, I answered that question in my previous post (admittedly very briefly).
I think the issue here comes down to a difference between a teleological explanation and an explanation of teleology.
Did you get a chance to read Neander’s Mark of the Mental? I’ve read the intro and wonder whether the body of the book has enough new to be worth the time to read (new with regards to the papers we’ve discussed).
Here is a short cartoon-like video on the PCR process. The DNA looks like twisted wires, the primers look like computer chips, and the nuleotides look like small plug in components.However notice that the polymerase is a pacman-like little figure with eyes and a mouth. The makers of the video must have thought that the polymerase was more lifelike than the other components to depict it in this way. The only thing needed for this procedure was to mix the ingredients under suitable conditions and the polymerase would go to work forming chains. One way to prevent the polymerase from carrying out this activity would be to kill it, in other words to denature it. A normal functioning polymerase is active, it is alive; a denatured polymerase is inactive, it is dead.
I didn’t say that crystallisation is a function. I said that crystals have some features in common with life. And I do not think that they are half alive.
How do you think life self-replicated before there were functioning polymerases?
Below is a diagram taken from this book published in 2002.
Here is the accompanying description:
What must it take to organise the production, ingestion, excretion, movement, and disposal of all these molecules? The cell is not just a bag of free floating chemicals, it is extremely well organised.
There is nothing magical about the vitalism I am speaking about, not in the way you mean.
What we do is observe and describe what we see. And what we see in the cell is molecular complexes taking up energy and displaying vitality. This can be described in terms of chemistry, but so can the movement of any living thing be described in his way. But does this explain purposeful movement such as kinesin complexes transporting substances to the cell membrane for export to areas where it is needed, does it explain why bees transport nectar back to the hive, or birds returning to their chicks with food? These activities can no more be fully described by chemistry as my words here can be described by the alphabet.
Denaturation is death? Say, my car stopped working and is inactive now; it is dead. Did I just prove all cars are alive?
That settles it: cars ARE alive:
Your claim was a bit stronger, since you said that crystals are a stage between static mixtures of matter and growing, differentiating life.
That you thought of crystallization as a function I deducted from your definition of having inner activity as “being able to ingest, convert and reuse energy in order to carry out a function such as movement or growth”. I assumed that the “growth” part was what made crystals stand out as being en route to living substance. If this is mistaken, I do not see how crystals of table salt fit in.
RNA world
Yes, cells are alive. I don’t see any disagreement here.
Is it possible it could be better organised? That diagram you posted looked like a mess.
For example, the Law of Demeter states:
Each unit should have only limited knowledge about other units: only units “closely” related to the current unit.
Each unit should only talk to its friends; don’t talk to strangers.
Only talk to your immediate friends.
The advantage of following the Law of Demeter is that the resulting software tends to be more maintainable and adaptable. Since objects are less dependent on the internal structure of other objects, object containers can be changed without reworking their callers.
As biology seems to be yet more complex then mere computer programs, why were similar guidelines not followed? That diagram shows lots of cross connectivity. When one thing changes, other remote things also change.
The cell may be extremely well organised, but could it be taken apart and put back together using our current design patterns? No, we can’t do that, but if we could I’m quite sure we’d end up with something totally different to what we have now. Something a bit less “spaghetti code”.
Since we are neck deep in the watchmaker analogy, it should be noted that spaghettiness is a positive sign of a system that evolved without top down design. Even when the system is known historically to be designed.
We know it was designed by fiddling.
Good question, that is what I would in fact say. Organisms are the way they are because their parts are the way they are, and those parts interact in the ways they do because of their properties, and their properties owe to what we call the laws of physics.
It explains why rocks are the way they are, why water is the way it is, why soap bubbles form and so on.
The why question that I think Mung wants to ask is this: why are some configurations said to be functional and others said to be malfunctional?. A causal explanation is insufficient: One can give the type of causal explanation you give in both cases for how the configuration processes inputs to outputs in a given context.
Now one has to avoid saying something like “it is malfunctioning when it is not working the way is is supposed to work”. Because hypothetical-Mung then gets to ask:: who determines how it is supposed to function? And he answers, the designer, of course. Of the Intelligent kind, naturally (or supernaturally, as the case may be).
So to avoid ID, we are just back to NS giving the appearance of design, which is basically what I posted way above, although I admit I preferred semi-humor to clarity. KN is going to the same place, but more articulately, I suspect..
Now hypothetical-Mung might say: I thought Darwinism is dead. Except he already did. Right, TSZ is a flat circle.
I haven’t gotten to it yet, but I can say that a friend of mine who works in neuroscience and the philosophy of neuroscience thinks that Neander’s book is the best theory he’s read of what representations are. I myself have some slight worries about the semantics part of teleosemantics. In my work on Sellars I try to give voice to doubts whether the same theory that explains how brains coordinate sensory stimuli and behavioral responses can also explain linguistic phenomena like de re and de dicto attitudes towards propositional content!
Thanks, I will spend more time with it then. I notice she does try to integrate second order resemblance (for explaining how content has causal power) with her updated teleosemantics, so that part will be new to me.
I agree about the gap between what she is doing and modern use of language. In the NBN interview with her, she admitted this book was about perceptual representations and her next would try to tackle concepts. So she seems to be working from bottom up to close the gap.
You agree that we can tell the difference between living cells and dead cells. What if a cell remained alive but ceased to function because proteins within it ceased to function? Would you not then say that the proteins had died?
This is an interesting article which looks at cell viability and cell vitality. They write:
We agree that the terms “alive” and “dead” do have meaning at the cellular level and above. But I do not see your problem with using these terms with regard to protein complexes such as dynein or polymerase. Metabolic activity is a measure of the activity of complex molecules such as enzymes. If you believe it is nothing but physics and chemistry then anything that displays an inner purposeful, organised activity could surely be classed as alive, and if it ceased this activity and dissipated into the environment then surely for all intents and purposes it is dead. We have seen that something can be said to be alive without it having to self-replicate. Or do you believe that there is some other difference between cells and protein complexes that gives justification for considering the former capable of being alive and the latter incapable?
How can I be anthropomorphizing when taking in and breaking down food is common to the whole animal kingdom not just humans?
I do think that both structural properties (second-order resemblance) and selection history are relevant, and that it’s not a matter of choosing one kind of explanation over another.
I have reservations about how well that kind of project can succeed, but I’ll withhold judgment until I see how she executes it.
CharlieM,
‘Dead’ and ‘alive’ have meaning at the level of cells and above, agreed.
But the distinction is not clear-cut: there’s alive, dying, freshly dead and completely dead. Your CFU quote illustrates the ‘dying’ category nicely: cells that still have some metabolic activity, but will die before they divide.
Anyone in cardiac arrest can be considered freshly dead; that’s how they teach CPR students.
Lyall Watson wrote (badly) about this grey “Romeo error” area in 1975, for a shorter and more compelling discussion, see this 1987 work.
But it makes no sense to apply these labels to proteins.
Proteins may be functioning, reversibly inhibited, irreversibly inhibited, or denatured.
Yes, researchers may colloquially refer to a non-functioning enzyme as ‘dead’; it doesn’t mean that the enzyme was ever ‘alive’, any more than re-naturing RNAseA is an example of “resurrection”.
Well from what I can gather from some people’s thinking, we should consider them to be alive. Why are they less alive than red blood cells?
IMO machines such as cars are conscious life’s early attempts to recreate itself. Dead matter is organised in such a way as to produce organised activity. This is a step on the way to life consciously producing life which is our ultimate technological aim.
You consider dead matter to be more fundamental than life, I think it is the opposite, life is more fundamental. We have no examples of life springing from dead matter but there are examples of dead matter coming from life, eg limestone and coal.
I think we have both seen that there is a certain amount of ambiguity in defining life. I would say that crystals are dead matter that has an inherent form which it retains during growth. Living forms grow but they also differentiate.
There are rather obvious differences between organisms and biomolecules, I daresay. Denaturation is a different thing from cell death and I just have this crazy thing about having different words for different concepts.
But as stated multiple times now, the definition of life is not set in stone. I really don’t care whether you include biomolecules into living things. It’s bloody useless and needlessly confusing IMO, but if that makes you happy than that is fine by me. What is problematic is that you are NOT talking about including organic chemistry but about some molecules having “inner [purposeful, organised] activity” without being able to clarify what the hell that means. To me it sounds an awful lot like élan vital, and I am not keen on swallowing that.
So once again: tell me what “inner activity” is. Is it selected biochemical function? That might properly describe both DNA polymerase and dynein function to the exclusion of e.g. urea function.
Fair enough. In that case you were just zoomorphizing again.
Well, I guess we need to upgrade the biology curriculum with some solid state physics and car mechanic classes then.
So you think that humans can do better than nature?
You are confusing the model with reality. The model appears to be a mess because it is a static 2 dimensional representation composed by humans who are ignorant of the complete picture, which is in part a 3 dimensional process taking place in time and designed to allow for further potential and to be in harmony and balance with a greater whole.
Some birds build nests which are a spaghetti-like jumble of twigs and whatever else they find lying around, but what they end up with is a beautiful, fit for purpose structure. If you were to zoom in to part of it you would see nothing but a jumbled mess.
It’s not anthropomorphizing per se, but it is a nice case of the metonymic fallacy: attributing to a part of a system a property that is correctly attributed to the whole.
A fiddling that has been able to sustain itself for billions of years if the time span is to be believed.
Kantian Naturalist,
Isn’t everything a part of the “whole”? Are you a different thing than the air which surrounds you? Is the air which surrounds you a separate entity from the sun?
If you zoom in close enough to your arm, is it a thing or is it space? When a neutrino moves through you is it a part of “you”. What about the bacteria on the outside and inside of you, is that you?
Because of the nature of matter, we are all just part of a cosmic soup of energy, there is no separation between anything.
Its why materialism can never be a valid worldview. How can something that is part of everything have a separate mind? Its unexplainable in purely physical descriptions.
How can the CPU in my computer calculate, when rocks in the ground can not?
I think there are different ways of looking at it, and it depends on perspective. I would certainly agree that there is a “whole”, the physical universe that we exist in and of which we are a part. Nevertheless we can still distinguish parts of the whole from each other. That they are “parts”, and that we could in principle imagine a “whole” without those parts, continuing to exist pretty much unaltered”. How would the entirety of existence be affected by my sudden absense? Not all that greatly. The celestial mechanics of the solar system, our galaxy, and the universe as a whole would continue. From a distant solar system, my sudden absense would be an immeasurable fact of no conseqeuence.
I think so, yes.
I think “me” stops approximately at the surface of my skin. That doesn’t mean everything below my skin IS me, but it can some times be.
Yes I think so.
It’s a thing.
It is not. The interactions between the parts that make up what I call “me”, and the neutrino, are too weak to have any effect on me. That is part of the reason for why they would not be part of me.
But I also think that “me” is transient, a fleeing, constantly changing entity. The only persistent fact is that I have the experience of “being me”. But I have changed in my life, and I continue to change. I change from one minute to the next, from one weeks to months, and over decades.
Many of them have very strong influences on me, and so would in turn constitute part of the explanation for why I am the way I am. That doesn’t mean they “are” me.
They can be PART of me, that doesn’t make them identical with me. They can be removed from me, and yet my experience of being me would persist, and other people would still be able to recognize me as “me”. So while they can be part of me, and contribute to the “me”, they cannot be said to BE me.
Being me, and influencing me, are not the same thing. Other people have an influence on me, that doesn’t mean they ARE me. That would be true even if materialism was false and if mind did not have a physical basis. It would still be the case, I think we can all agree, that different minds have influences on each other. The actions you take, the words you say or type, and which I hear or read, influence what I think and what I do, and the other way around. Are you and I therefore the same thing, one and the same person? I don’t think so.
I don’t see why that follows. I would agree with you so far as to say that exactly delineating where entity X stops and Y begins at the subatomic level can be very difficult, and may seem arbitrary, but it does not follow from this that such distinctions are impossible or meaningless.
It is like saying there is no way to tell where the water in my cup stops, and where the inner surface of the cup begins, and so they are the same things. But they clearly aren’t the same thing, and we CAN tell the difference. There are measurable properties of the water molecules that make them recognizable as water molecules, and part of the bulk of liquid we call water, and not part of the cup itself.
Looks just like my code. It’s like anti-IDer’s have a sort of reverse complexification mania. It looks complicated, must be spaghetti!