False. Evidence of precursors that had completely different functions exist. In contrast, there is zero evidence of Behe's theory supports it. Behe also makes assumptions that structures must work well or efficiently in order to be of value to the organism. False, because nature is full of examples of clumsy and imperfect structures that merely get by. Oversimplified with a false premise. This is an unoriginal creationist vlog.
"Evidence of precursors that had completely different functions exist."
But that's not the point of my video (I take it that you DID watch it?). I'm not even saying that IC systems cannot evolve. All I am saying is that scaffolding and Elimination of Functional Redundancy do not offer general solutions to the origin of IC molecular machines. BTW, I'm not a creationist.
I used the analogy of the bridge to show how scaffolding works, and how, in isolated circumstances, it can generate IC systems. The reason I'm starting with just one component, A, at 3:45, is because I am showing that scaffolding does not offer a general solution to the origin of IC systems that carry out functions which require multiple interacting components.
@Genomiques I understand the point of your argument. I am the false application of the bridge analogy. Component A is only part of the bridge and is not forced to have the "bridge" function, yet you start your argument by forcing A to have the complete function, thus there is the fallacy of equivocation. You are stating that component A of our second model is analogous to the component A of the bridge, but clearly it is not.
The analogy of the bridge is merely to show how scaffolding works to create IC systems. I am not stating that component A of the biological model is analogous to component A of the bridge. Forget the bridge. It is only useful as an explanation of how scaffolding works.
@Genomiques You use the bridge as a demonstration of scaffolding, and then state that its biological equivalent is the ABC block with helper D. You then say, "Thus, for scaffolding to explain the origin of that IC system, we must start with only one component, A, carrying out the function." WHY? You just gave us the analogous physical system that used ABC as the functional unit, and you showed how it was made IC using scaffolding.
I don't state that its biotic equivalent is the ABC block with helper D. When I said "biologically, this can be represented" I meant: "biologically, the concept of scaffolding can be represented with these blocks." Since the ABC complex is already IC, we must explain this system with starting out with just one component, A.
@Genomiques Okay, so you create an alternate representation of bridge ABC. You then show how through one addition and one deletion process, a new IC. None of these systems have one component. You then assert: we must explain this system starting out with just one component. Again, WHY? You just started with a three-component system and through scaffolding, created a new IC system. What is your basis for artificially constraining the system to one component?
If you start with a system that consists of three components, then you've got to also explain the origin of that three-part system. If you take a look at 3:00, you will see that A, B, C, are all necessary to the function, while D is not. This means that A,B, and C form an IC system. So does scaffolding explain the origin of that IC core consisting of components A, B, C? Not if the function is dependent on the interaction of multiple components.
@Genomiques I entirely agree that scaffolding does not explain the origin of the ABC bridge, but three components can easily come together to form a useful function. You are arguing that scaffolding cannot account for larger systems, by making the assumption that we must start with a single component with the full function. This doesn't even take into account how the function changes over time. Proteins often have more than one active site. Some for activity, and some for regulation.
"But three components can easily come together to form a useful function."
Not really, because if they came together all at once to form a useful function, then you need a number of specific, simultaneous mutations occurring. The odds of that happening are next to nil. That's why you don't see any real-time instances of three component molecular machines evolving.
@Genomiques [you need a number of specific, simultaneous mutations occurring] This was the exact blunder Behe made that I was trying to warn you not to make.
Actually, davidmcaba was suggesting that a three-part IC system could evolve all at once by all three components coming together all at once. And this is highly unlikely because this would mean, by definition, that a number of specific mutations would occur simultaneously. The odds of a three part IC system coming together all at once are next to nil, which is why H. Allen Orr et al. repudiate that view.
@Genomiques Two is still a very small number, and there's no requirement for them to be simultaneous, nor did david say they needed to be. If one non-detrimental mutation occurs, then a million years pass, then another mutation occurs, you'd have this scenario. Any claim of "unlikely" cannot just be asserted. It must be justified. No one doubts it's unlikely to some extent, or we'd see it happening daily. That's different than asserting it's so unlikely that it could not have happened at all.
Yea but you're assuming that just two mutations would be needed. If we're starting with proteins that carry out entirely different functions, which means that they are usually localized in different subcellular locations, probably more than one mutation would be needed to shift its localization.
@Genomiques Can you provide a link to Orr's statement on this you're referencing? I looked and only found affirmation that IC systems have been observed to evolve via gradual adaptation, citing Muller's work.
"...it will do no good to suggest that all the required parts of some biochemical pathway popped up simultaneously by mutation. Although this "solution" yields a functioning system in one fell swoop, it's so hopelessly unlikely that no Darwinian takes it seriously. "
- H. Allen Orr, Darwin v. Intelligent Design (Again): The latest attack on evolution is cleverly argued, biologically informed - and wrong.
@Genomiques Orr said Behe is suggesting all the required parts must pop up simultaneously.
Everyone agrees that several mutations "in one fell swoop" is unlikely. That's irrelevant since everyone also agrees mutations need not be simultaneous.
With "two mutations", I was simply referring to the example given. Any number of mutations can happen this way, and since there's no "end goal" in mind, any beneficial combination is allowed, which is far more likely than any 1 specific chain of mutations.
@Genomiques No; it is not impossible for three mutations to occur, and they don't have to be simultaneous. Mutations occur over time, and neutral mutations may later become useful. Please note in your example of the bridge that A and C are not needed, only B, but later, A and C are essential with D, and B is no longer in the picture.
"No, it's not impossible for three mutations to occur."
Of course, I never claimed that o.o
But, if I understand you correctly, you are suggesting that system ABC could have arisen in one fell swoop, with all three components coming together, forming a novel function. And that's unlikely.
No, it's not all that unlikely for you to toss a quarter and receive a head three times in a row. The odds of that happening are 1 in 2^3, or 1/8. Quite likely, actually. This is not the same odds for three specific mutations to occur, giving rise to a novel function.
@Genomiques Great, now how unlikely is it for three components to come together to form a function?
Also, please note that you've already asserted that it could happen with the bridge example. ABC are three components, to which you added D and subtracted B, and now you have a three-component IC system.
It depends on the components, and where the original components are localized in the cell. If the components are localized in different sublocations in the cell, then almost certainly more than one mutation will have to occur to each component to bring them to a new cellular location.
@Genomiques Also note, in the original idea of the bridge, none of the parts are forming a bridge. They are simply three parts lined up. The addition of D and subtraction of B creates the bridge function.
@Genomiques No, the original idea of a bridge forming from scaffolding has three parts that are not a bridge. The addition of D and subtraction of B forms the bridge. In your modified example, you have started with a bridge, and modified it to form another bridge.
The function of the bridge is to arise from the process, not be assumed at the start.
@Genomiques Because you cheat the example by giving the system the function from the beginning. The real example show how the bridge function arises from the scaffolding process. This is the heart of the issue. You say scaffolding cannot produce multi-component IC systems, yet this is precisely what the bridge example demonstrates.
No, it's not, 'cause the only reason I use the bridge is to demonstrate how scaffolding works to create IC systems. Scaffolding cannot produce multi-component IC molecular machines without the invocation of cooption, if those molecular machines carry out functions that require multiple interacting components in order to exist.
@Genomiques You are simply stating your thesis. I have already shown two errors in your presentation. 1) You incorrectly present bridge scaffolding by giving the bridge function to the initial ABC system, when it is supposed to arise from the ADC system that arises from the ABC system through scaffolding. 2) You continue this error by false attributing the full function to a single component, which is the cornerstone of your argument.
"A clear example of the Mullerian two-step [which is essentially scaffolding] is given by a stone bridge. Consider a crude 'precursor bridge' made of three stones. This bridge spans the area needed to be crossed and is thus functional. For step one of the Mullerian two-step, a part is added: a flat stone on top, covering all precursor stones. Whether this improves the functionality of the bridge is irrelevant..."
"Why Behe's 'Irreducible Complexity' is Silly," TalkOrigins
Finally, I have already said many times that I am ONLY using the bridge example as an example of how scaffolding works. There are many biological functions which can only function through the interaction of multiple components. Such systems cannot arise through pure scaffolding because you'd have to start with one component, but one component cannot carry out the function. If you invoke changes of function, then you're using cooption as your explanation, not scaffolding.
We must start with a single component because otherwise you're starting with multiple components which all fortuitously came together, which is highly improbable - evolutionary biologist H. Allen Orr acknowledges that, e.g.
"This doesn't even take into account how the function changes over time. Proteins often have more than one active site."
If you still want to use the bridge as an analogy, then you will notice that the bridge starts out with three components in the first place. If the bridge was a biological entity, then its evolution would have to occur step-by-step, starting with just one component imparting a beneficial function to the organism.
But how did it fall apart? Your criticism was that he started making unsupported claims that fell apart. But you haven't substantated your claim that these arguments made in the video (after 3:25) actually did fall apart.
But perhaps you can list some reasons why you believe that these claims fall apart after 3:25?
"However, while scaffolding may explain the origin of some IC systems, it fails as an explanation for the origin of IC systems whose function depends on the interaction of multiple gene products."
How is this an unsupported assumption? At 4:50 I present a small sample of molecular machines that carry out functions which require multiple gene products. This is not an unsupported assumption. So, please tell me, where are my unsupported assumptions after 3:25?
@Genomiques An example of one place where you, personally, can't think of how something may have happened, doesn't show it's impossible. Perhaps you're just not clever enough to figure it out. (Perhaps no one is, but that doesn't make it impossible or even improbable.) As it turns out however, biologists, (the people that understand this the best), have no problem whatsoever seeing how it happens, for this example.
Keep in mind that the multiple genes don't have to have evolved at the same time.
"An example of one place where you, personally, can't think of how something may have happened, doesn't show it's impossible."
Yea but you're ignoring my question. Where exactly does my video break down and how does it? What I am doing here is showing how scaffolding and elimination of functional redundancy doesn't offer a general solution to the origin of IC molecular machines. This isn't lack of imagination on my part, otherwise you could simply respond to the actual arguments.
"Perhaps you're just not clever enough to figure it out."
Figure what out? Again, I am not making an argument from imagination here. My arguments in this video are supported by real biology. The point of this video is not that Darwinian mechanisms cannot explain the origin of IC molecular machines. The point is that the specific pathways of scaffolding and Elimination of Functional Redundancy don't work. Respond to those points, rather than go after a red herring. Thanks.
@Genomiques [Duh] Well, Behe doesn't know that, so I'm not assuming anything.
What "real biology" is your video using? Yes, you assert scaffolding doesn't work, but you haven't supported it with biology. You supported it with assertions that it doesn't work.
@3:25 You support the assertion "fails...whose function depends on...multiple genes" with an argument based on the assertion "must start with one component".
@3:44: What "real biology" supports "we must start with only one component"?
I don't think you quite understand the video. In the scaffolding scenario, components A + B + C are necessary to the molecular machine, while D is helpful but not necessary. D then becomes a necessary component as the system evolves. But this scenario already starts with an IC system: A + B + C, so how does scaffolding explain the origin of that IC core? (continued)
@Genomiques Yes. I understand that just fine. It's irrelevant. You're setting up a scenario which you can easily refute, while ignoring the point of the argument. If you're just going to say a+b+c is IC, then make your scenario discuss a+b+c. Adding D just sets it up so you don't have to address the point. For your argument to make any sense, you'd have to assume that ALL configurations a+b+c are IC. They're not, of course, so why make it a requirement? All systems a+b are not IC.
"If you're just going to say a+b+c is IC, then make your scenario discuss a+b+c..."
Gee whiz. I did exactly that. Did you watch the video? See 3:43 through 4:30. You didn't SERIOUSLY think that my refutation of scaffolding as a general solution to IC is simply "we're already starting with an IC system, so scaffolding doesn't work." No, my refutation is more elaborate than that.
So, in the scaffolding scenario, how do we evolve an IC system that requires components A + B + C? We would start with one component, A, which later becomes necessary to the function. If we start with two components, say, A + B, then that system is already irreducibly complex, and so scaffolding must explain the origin of *that* IC system (continued).
If, on the other hand, A + B are helpful, but not necessary components - the A+B system not being IC at first, then - we run into the problem that there are a whole bunch of biological functions out there that demand the interaction of multiple gene products; i.e., A+B would be necessary. And so scaffolding would have to account for the origin of that IC system. See the problem? Try to visualize what I'm saying here and then it may be clear.
@Genomiques And the problem with "multiple gene products" is what? Why couldn't A and B be present but not necessary? Then a+b+c become present and performs a new function, which was not preformed by A and B alone? a+b+c thus become required for the new function, but not required for the survival of the organism.
"And the problem with 'multiple gene products' is what? Why couldn't A and B be present but not necessary?"
Here's why: if we're using scaffolding to explain the IC state of molecular machines whose very functions require the interaction of multiple gene products - I present a small sample of such machines in the video - then A+B must be necessary because the function REQUIRES interaction of multiple gene products (continued).
@Genomiques You're overly complicating the explanation by bringing up A+B+C+D. Your stated initial condition is that A+B are required for function X. Therefore A+B is IC with respect to function X. Then you simply assert that A+B couldn't have been placed there via a scaffold @4:27.
@4:27 you seem to be assuming that function (A) and function (A+B) are identical. If function (A+B) can't be carried out by A alone, then it's irrelevant to your argument and you shouldn't need to bring up A at all.
"...you seem to be assuming that function (A) and function (A+B) are identical."
Yea because otherwise we'd talking about cooption, not scaffolding. In a purely scaffolding scenario, no change of function would take place: that's called cooption. This video does not address cooption, and so it doesn't invoke cooption.
"If function (A+B)can't be carried out by A alone, then it's irrelevant to your argument..."
No, that's the POINT of my argument. The POINT of my argument is that scaffolding doesn't explain the origin of IC molecular machines that carry out functions which, by their very nature, require the interactions of multiple components. Thus, pure scaffolding cannot explain the origin of such IC molecular machines - and there are a fairly large number of them.
@Genomiques Now you're just making claims based on semantics, not logical thought or science. It doesn't matter that scaffolding exists along side other mechanisms. IC systems still evolve, and scaffolding is heavily involved. You seem to have just eliminated any purpose to your video.
Your original comment was "this video explaining why evolutionary pathways have a hard time explaining the origin of IC molecular machines". This video doesn't show anything of the kind.
No, my arguments have nothing to do with semantics. The point of this video is that pure Scaffolding and pure Elimination of Functional Redundancy cannot feasibly offer a general solution to the origin of IC molecular machines.
"It doesn't matter that scaffolding exists along side other mechanisms."
Oh yes it does, 'cause if you're going to be invoking cooption then why invoke scaffolding? It's superfluous to do that (continued).
"You seem to have just eliminated any purpose to your video."
The purpose:
To explain why scaffolding and Elimination of Functional Redundancy do not sufficiently explain the origin of IC molecular machines. Cooption would have to be invoked, and if you invoke cooption along side scaffolding, then why invoke scaffolding? You're not being logical now, are you?
@Genomiques Then you failed. Your argument is incoherent. Your explanation here in the comments section hasn't clarified your position.
A to A+C to A+C+B to A+B is quite sufficient. That's scaffolding without a requirement for cooption. Plus, even if cooption is required, that doesn't mean scaffolding doesn't happen and/or isn't involved.
I've already responded to this line of thought many times, yet you are still unable to get it. If A to A+C share the same function, then this does NOT work if we're talking about the origin of an IC molecular machine whose function REQUIRES the interaction of multiple components. I.e., that function could not be carried out just by A. (continued)
Now, if A and A+C do not carry out the same function, then you're invoking cooption, so using scaffolding alongside cooption is superfluous. So your comment "that's scaffolding without a requirement for cooption" has been thoroughly responded to: scaffolding, without cooption, cannot explain the origin of IC molecular machines - and read this carefully - that carry out functions which, by their very nature, require the interaction of multiple components. (continued)
And that is the point of my video: that the scaffolding pathway is does not explain the origin of that large number of molecular machines that carry out functions which require the interaction of multiple components. The function of bacterial motility through Brownian motion cannot be accomplished with just one component, A. So starting out with A, then A+C does not work. And if a shift of function occurs, you're invoking cooption.
Which means, again, that your statement that "that's scaffolding without a requirement for cooption" is incorrect with regards to the core argument in this video.
"Plus, even if cooption is required, that doesn't mean scaffolding doesn't happen and/or isn't involved."
Quite true, but if cooption is required, then invoking scaffolding is simply superfluous and doesn't by itself explain the origin of the IC system. Which means that cooption is the only viable evolutionary route.
@Genomiques If cooption occurs, that means scaffolding is superfluous? Do you think they're mutually exclusive in the universe? Cooption disproves scaffolding? What an odd thing to assert.
"If cooption occurs, that means scaffolding is superfluous?"
If cooption is REQUIRED for the origin of an IC molecular machine, then invoking scaffolding isn't necessary. The two are obviously not mutually exclusive, but that's not the point. The point is that just because scaffolding plays a role in modifying an IC system that was evolved by cooption doesn't mean that scaffolding is a feasible explanation for the origin of IC molecular machines (continued).
You still don't seem to be getting the point of this video.
Just answer this simple question, with a "yes" or "no" answer, and provide explanations if the answer is "yes."
The question is:
Is scaffolding alone a feasible evolutionary pathway for the origin of IC molecular machines whose functions require the interaction of multiple components?
@Genomiques Quite right. I see no point to your video.
Who cares if scaffolding alone works? I don't. Biologists don't. You shouldn't. It's an irrelevant point. Evolution of IC systems happens regardless of the answer, which is why it's an irrelevant question.
Yes, scaffolding alone is a feasible evolutionary pathway for any system, IC or not. I gave you the general progression already. There's no indication of cooption in my statement. Cooption may or may not be present.
"Who cares if scaffolding alone works. I don't [you're no biologist]. Biologists don't [oh yes they do]."
If scaffolding alone doesn't work, and if Elimination of Functional Redundancy alone doesn't work, and if cooption alone doesn't work, then there is no viable evolutionary pathway for the origin of IC molecular machines. Your inability to grasp this concept is, well, plain absurd o.o
"Evolution of IC systems happens regardless of the answer, which is why it's an irrelevant question."
Indeed? Then I should like to know how IC molecular machines evolved through non-teleological mechanisms, without your invoking scaffolding, Elimination of Functional Redundancy, or cooption. If you don't provide a mechanism, then you must concede that if we eliminate the viability of those three pathways then Darwinian evolution does have a hard time explaining IC machines.
Here's why your general progression for scaffolding, in the absence of cooption, doesn't work for the origin of that large number of IC molecular machines whose functions require the interaction of multiple components:
If the FUNCTIONS of those IC molecular machines REQUIRE multiple components, then starting with component A carrying out the function is impossible since the function cannot work with just one component like A. (continued)
@Genomiques It doesn't matter how many components are required. That's where I began by saying you need to stop assuming things. Scaffolds can be as complex or as simple as you'd like. Scaffolding still happens.
You haven't "roundly thrashed" anything. You've simply restated you initial assumptions as if they're correct. It was wrong the first time you asserted it, and it's still wrong now.
A+B may perform the exact same function as A: no cooption. A+B could be a brand new function: no cooption.
"It doesn't matter how many components are required."
Oh yes it does. If an IC molecular machine carries out a function that requires the interaction of multiple components, then your scaffolding scenario starting out just with one component, A, doesn't work *because the function cannot exist with just one component.* And IF you say that component A isn't carrying out the same function as A+B, then you are invoking cooption, which means pure scaffolding doesn't work.
"That's where I began by saying you need to stop assuming things."
The only thing I am assuming - and this assumption is backed up by a number of clues - is that you lack a college level education in any biological discipline.
"Scaffolding still happens."
I never denied that. However, as this video argues, pure scaffolding does not offer a general solution to the *origin* of IC molecular machines.
"A+B may perform the exact same function as A: no cooption."
Of course, this does NOT work because if A+B performs the same function as A, and if that function by its very nature can only exist by the interaction of MULTIPLE components, then a single component, A, by definition, cannot carry out that function. Your problem is that your starting out with only one component, but many biotic functions can only exist through the interaction of several componenets. Try again o.o
And of course, that's the point of this video: that pure scaffolding cannot feasibly explain the origin of that fairly large number of IC molecular machines which carry out functions which require the interaction of several components. That is THE point of this video. You have been unable to refute that point, I'm afraid.
@Genomiques If your point is restricted to what you just said, then my overall response is "so what"? The evolution of IC systems is not claimed by anyone to rely solely on scaffolding. I've refuted it. You just missed the point because you're still operating under the mistaken assumption that your claims are accurate.
"If your point is restricted to what you just said, then my overall response is 'so what'?"
My point IS restricted to what functions which require the interaction of multiple components in order to exist, and your realization only now that this is my point is a bit absurd o.o
Since such functions cannot be evolved via scaffolding and Elimination of Func. Redundancy, then the only viable route is cooption, correct?
@Genomiques [Since such functions cannot be evolved via scaffolding and Elimination of Func. Redundancy, then the only viable route is cooption, correct?] Wrong. Evolution of a particular function can involve any or all of those. Those words and concepts exist because they've been observed to occur. To claim they don't occur is absurd, and I said so in the beginning.
"Wrong. Evolution of a particular function can involve any or all of those."
We're not talking about the plain ole' evolution any ole' function. We're discussing the origin of IC molecular machines which carry out functions that require multiple interacting functions in order to exist. Pure scaffolding cannot explain the origin of such systems, and so cooption must be invoked. In short, in the absence of cooption, such functions cannot evolve.
@Genomiques There's no established difference between the evolution of IC systems and non-IC systems. If you disagree, then explain how they differ. (Don't just define it. I already know that "if you remove one part" definition that's meaningless.)
"There's no established difference between the evolution of IC systems and non-IC systems."
Actually, when it comes to molecular machines, there is a difference. If a molecular machine's function is not IC, then it could have evolved through gradual improvement upon one, same function. However, this doesn't work if a molecular machine is IC: you must propose a different pathway to account for the IC state of the system.
@Genomiques Oh? How so? In what way can an IC system not evolve in a gradual step-by-step way using the very mechanisms you've outlined in your video? To avoid your assertions we've already discussed (to no avail), what if all these mechanisms are involved in all evolutionary processes? You haven't claimed that scaffolding plus cooption can't produce IC systems, have you? (If you did, you're wrong, of course.)
"In what way can an IC system not evolve in a gradual step-by-step way using the very mechanisms you've in your video?...what if all these mechanisms are involved?"
I've demonstrated that scaffolding alone does not offer a general solution to the origin of IC machines, and so if scaffolding alone doesn't work then you have to invoke cooption. Which means that cooption + any optional mechanisms is the only viable evolutionary pathway for the origin of such systems.
Remember, the point of this video is this: *scaffolding alone does not explain the origin of IC molecular machines which carry out functions that require multiple interacting components in order to exist.* Do you, or do you not, agree with that statement?
@Genomiques And remember I've already opined the point of this video is meaningless.
No. I don't agree. Scaffolding is involved and you haven't shown otherwise. You've claimed scaffolding alone does not produce IC evolution (wtf is a machine in this context anyway?). You haven't shown, and in fact have stated, that scaffolding IS involved in evolution.
[Which means that cooption + any optional mechanisms is the only viable evolutionary pathway ] And what would that imply?
Yea but it's not meaningless, because if scaffolding and EFR alone cannot explain the origin of such IC machines, then you must invoke cooption. Which means that cooption is the only viable pathway for the origin of such systems.
So you do not agree that *scaffolding alone does not explain the origin of IC molecular machines which carry out functions that require multiple interacting component in order to exist*? Then please explain how, in the scaffolding scenario, you can start with one component, A, carrying out Function X which requires multiple components in order to exist?
@Genomiques [explain how, in the scaffolding scenario, you can start with one component, A, carrying out Function X which requires multiple components in order to exist?] I already have, but... here's one:
Protein A (to clarify what "A" is) performs no function whatsoever by itself. Protein B performs no function whatsoever by itself. But A+B performs function X. No cooption involved. (No scaffolding involved either, but your question was about how the original two components can have existed.)
I compliment you on your imagination but I am disappointed in your ignoring of natural selection. If proteins A and B performs no functions, then random mutations will hit those genes, and natural selection will probably eliminate them from the gene pool. But assuming this doesn't happen: my question actually was not how the original two components could have existed.
@Genomiques [then random mutations will hit those genes, and natural selection will probably eliminate them from the gene pool.] Why would RM eliminate those genes? The error rate in gene reproduction is 10^(-8), which means it'd take millions of generations before it's likely to be eliminated. Within the time span of those generations, the other DNA sequence mutation would be relatively likely. Keep in mind that random mutation happens trillions of times a second throughout a large population.
Random mutations would hit those genes, destroying their sequence identity, which means that they probably won't be able to carry out any future function. On top of that, it's natural selection that would eliminate functionless genes from the gene pool, in bacteria anyway, since with unicellular organisms their is a cost associated with keeping genes that carry out no function, especially if those genes are translated.
My question was how only one component, A, can carry out a function that REQUIRES *multiple* components in order to exist. That IS the question. That's why my question is relevant to scaffolding, while the scenario you just outlined really isn't.
Scaffolding is involved in evolution. But scaffolding does not explain the ORIGIN of IC molecular machines whose functions require the interaction of multiple component. Scaffolding can modify that system, but it does not explain the ORIGIN of that system. Simple concept, right?
@Genomiques [That scaff. and EFR alone are not adequate...for the origin of IC machines, which means ...cooption.] And, in turn, what would that imply?
Answer my question about the difference between the evolution of IC systems and non-IC systems. You can't even define an IC system in terms of mechanisms. You can only define it (as Behe did) as a system where taking away one part changes the function. That's true of virtually ALL systems, biological, mechanical or otherwise, is it not?
An IC system could not have evolved through gradual improvement of one function. For example, consider a system that I would not consider IC: the giraffe's neck. The giraffe's neck evolved through gradual improvement upon the length of the neck. Now, if a system is IC, then the pathway of gradual improvement of one function doesn't work because elimination of a part results in a different function, meaning that evolution must work on different functions.
@Genomiques [An IC system could not have evolved through gradual improvement of one function. ] Not true. But so what? Say I grant you this. Now what? Say I also grant that in an IC system requires that an added protein that changes the function (cooption). Then what?
Then what? Well, what if, upon further analysis, the cooption scenario also breaks down? Then what? You don't have a viable evolutionary pathway for the evolution of IC molecular machines.
@Genomiques [what if, upon further analysis, the cooption scenario also breaks down] Why? Are you likely to present such an argument? (<== bad attempt at Douglas Adams humor). If you could show that no combination of scaff, EFR, and cooption works, then you're left with all the other mechanisms which you haven't included in your argument. Any of these unknown mechanisms could be the actual mechanism used. It's nearly impossible to prove a negative, so your work is cut out for you.
"Then you're left with all the other mechanisms which you haven't included in your argument..."
By "other mechanisms," I suppose you mean unknown mechanisms which you think they must be there? They may be there, but since no one knows where we might find these guys, non-teleology is no longer the default explanation.
@Genomiques [You shall see what you shall see] Then you should have started with that argument. Presenting a video without a meaningful purpose isn't helping anyone. The main problem with your video here, aside from a lack of obvious purpose, is that it's not even making a convincing argument for the elimination of scaffolding or EFR. You've simply presented the scenarios you feel you can shoot down (yet you failed to do so), and you've ignored the fact that these mechanisms are know to occur.
"..and you've ignored the fact that these mechanisms are known to occur..."
You seem to have a hard time grasping the concept that even though these mechanisms occur doesn't mean that they explain the origin of all IC molecular machines. For example, neither EFR nor scaffolding alone could explain the origin of the bacterial flagellum.
@Genomiques [ the concept that even though these mechanisms occur doesn't mean that they explain the origin of all IC molecular machines] Using another creationist argument? I've asked, but have not received, your explanation of how you think the mechanisms of IC evolution differs from any other evolution. Biologists (the people that understand this stuff the best) see no difference. It's creationists that need to ignore observation and invent new terms, like ID and IC to confuse people.
@Genomiques [For example, neither EFR nor scaffolding alone could explain the origin of the bacterial flagellum.] Biologists don't say any one mechanism alone does explain the BF. You're arguing against a claim no one makes. Here's one detailed description of how standard evolutionary biology can be used to explain the BF:
talkdesignDOTorg/faqs/flagellum.html
[asserting unknown evolutionary mechanisms] Only known mechanisms are asserted. We leave unknown mechanisms to theists :)
"Biologists don't say any one mechanism alone explains the BF..."
Actually, cooption is the only mechanism used to explain the IC core of the bacterial flagellum. Regarding your link, I could in fact show you exactly where that pathway breaks down (well, it breaks down at the beginning), but I can hardly do so in 500 characters.
@Genomiques Btw, I'm not asking "and what would that imply" to be pedantic. I'm trying to get to the root cause of your belief that your video discusses a meaningful point. To cut to the chase, assume I grant you all your claims. Why is any of this important? What end message are you going for, and why is it important to our understanding of evolution? Say, for the sake of argument, that scaff, EFR, and cooption are all required for all evolution and no evolution could occur without cooption.
Firstly, keep in mind that I am discussing this from the angle of molecular machines. You say "and no evolution could occur..." Well, I'm not attacking the theory of evolution at all. I'm analyzing the concept that IC molecular machines evolved through scaffolding, EFR, and cooption. (continued)
So, to cut to the chase, if the evolution of IC molecular machines could only occur through cooption, then if we find cooption ALSO to be an inadequate explanation for the origin of those machines, then there's really no satisfactory non-teleological evolutionary explanation for the origin of those machines. This video doesn't discuss cooption because it's a topic all of its own.
@Genomiques Your examples specifically rule out any discussion of cooption+scaffolding+EFR, so you still haven't shown that evolution of IC systems is impossible. You've only shown (if you were to show) that more than one mechanism is involved. Also, you've ruled out any discussion of any other mechanisms that may be involved of which you just aren't familiar. All you've done is arrived at the basic teleological argument for God, which is essentially an just an argument from ignorance.
My discussion only shows that scaffolding and EFR can only explain an IC molecular machine is cooption is involved. That was the point of this video, and I will discuss cooption in another. If we rule out the viability of cooption, then cooption+scaffolding+EFR doesn't work either, because the viability of all three pathways has been eliminated.
@Genomiques Natural selection would only eliminate detrimental sequences, not neutral ones. Most mutations are neutral, neither beneficial or detrimental, which is why "junk DNA" stick around for so long. Look at the largest genome, the amoeba dubia. If you are right, then the DNA sequences would have long since disappeared. Why didn't they?
I get the feeling that we're going off on an unimportant tangent. But anyhew, the amoeba's genome is mostly untranslated nucleotide sequences, which means there isn't a negative cost associated with a large genome. But if all those sequences were translated into amino acid sequences, then there would definitely be a metabolic cost, especially for unicellular organisms.
Feel free to list another evolutionary mechanism other than cooption, scaffolding, and EFR that might explain the origin of IC molecular machines. And I didn't mention any gods or deities - you're automatically assuming I'm a theist, it seems, never considering the possibility that I may actually be an agnostic or an atheist or one of those who simply don't care if gods exist or not. Also, IC in itself is not positive evidence for teleology.
@Genomiques [Feel free to list another evolutionary mechanism other than cooption, scaffolding, and EFR] And what if I can't? Does that mean there aren't any? For your argument to prove anything, you'd have to know for sure that there aren't any. "Because I'm not smart enough to think of one" is not a valid argument. You'd have to show, there are, in fact, no others. You haven't shown this.
You mentioned teleology, which is a standard argument for God. I didn't assume anything.
Right, and I suppose if we found a metallic pyramid-shaped object floating in space it would be illogical to conclude that it was designed because there might be non-telic mechanisms that we can't think of that would explain its origin?
"You mentioned teleology, which is a standard argument for God."
I think I've explained this to you before. By "teleology" I mean exactly what it means: a purposeful, goal-oriented mechanism. The word "god" isn't even part of the definition.
@Genomiques [teleology] Then my mistake. Both IC and the teleological argument are very common creationist arguments for the existence of God. When you use the terms, you must expect that people will conclude that your end goal is to disprove evolution and posit a God is required. Especially when you've not been forthcoming with why you're going down this road in the first place.
"Especially when you've not been forthcoming with why you're going down this road in the first place."
I'm doing my best to approach the discussion of biological origins with as much objectivity as I can. And so I readily admit that, contrary to what many creationists say, IC in itself is not a positive indicator of intelligence. So too, I often wonder why non-teleologists like yourself don't find the existence of a genetic code, e.g., at least SUSPICIOUS of intelligence.
@Genomiques [IC in itself is not a positive indicator of intelligence] Finally something we can agree on.
I don't find the genetic code indicates an intelligence for two main reasons:
1. I understand how the code would naturally develop via RM and NS.
2. An intelligence which did not develop in a way consistent with biology and physics would need an insurmountable amount of explanation ... an explanation much more complicated than the evolution of systems you're trying to explain.
"I understand how the code would naturally develop via RM and NS."
Keep in mind that just because something *can* evolve through non-intelligent mechanisms does *not* necessarily reflect its true history. Just saying.
"An intelligence which did not develop in a way consistent with biology and physics..."
You are, of course, assuming that an intelligence would not have developed in a way consistent with biology and physics.
@Genomiques [Keep in mind that just because something *can* evolve through non-intelligent mechanisms does *not* necessarily reflect its true history] And again, we can agree. Yet, positing convoluted unknown and untestable mechanisms when known physics and biology provide the mechanisms, seems unnecessary. Perhaps rainbows *are* created by supernatural or unknown mechanisms, but that's no reason to ignore optics.
@Genomiques FL is testable? Not in the least. Your video claims it's testable, but didn't bother to show this is true.
You can't show what this video purports to show, so I doubt very much that you can show exactly where my linked article breaks down.
Your linked paper says that evolution of IC systems is possible. How does that support your claim? (It doesn't define IC any differently than Behe did however. My question is how you'd identify an IC system, which the paper states is unclear.)
I'll reserve the particular discussion for another day, but of course, any one with any real training in biology could see how we could test that hypothesis.
"You can't show what this video purports to show..."
Oh yes I can, and I have. You haven't refuted anything. Your inability to grasp basic concepts isn't a reflection of my intelligence but yours.
You seem entirely incapable of understanding, for example, that one component, A, cannot carry out a function that requires multiple interacting components to exist. This is a simple concept, but you can't get it, can you?
"Your linked paper says that evolution of IC systems is possible."
Of course, I never denied that. The paper also explains why the evolution of IC systems require different mechanisms than the evolution of nonIC systems. Your comprehension skills aren't that bad?
It *talks* about Darwinian mechanisms, but it also says that serial direct Darwinian evolution - change along a single axis - cannot generate irreducibly complex systems.
@Genomiques The question was how you can tell what an IC system is in terms of mechanisms. The answer is there is no difference in the mechanisms. The same mechanisms which result in IC systems are also used in all evolution. The mechanisms aren't any different, although the paper does say some mechanisms by themselves won't yield IC systems. This is not the same as your claim (that no mechanisms exist which will yield IC systems). This paper refutes your claims, so I question why you linked it.
Although all mechanisms used in the evolution of IC systems can also be used in the evolution of non-IC systems, the reverse is not true: all mechanisms used in the evolution of non-IC systems cannot all generate IC systems. Please tell me exactly where I claimed that no mechanisms will yield IC systems.
@Genomiques Sure. That's fine. Some mechanisms by themselves wouldn't result in IC systems. So if you agree that IC systems can evolve, then I'm still missing the point you're trying to make. If your only point is that more than one mechanism is involved, and no one is making claims that only one mechanism is involved, then we're back to this video having no point. Who cares if cooption is required along with scaffolding, ERF or other mechanisms? Your answer was that you'll make another video.
Well, if cooption is required to generated IC molecular machines that carry out functions which require multiple interacting components, then if we find that cooption also fails as a general solution to the origin of IC molecular machines, we must conclude that there are no known, robust, non-teleological explanations for the origin of IC molecular machines.
@Genomiques You were wise to add "known" in your conclusion. So, if you could show cooption was both required and inadequate (two tings you have yet to show), then you're left with some unknown (to you) mechanism, a combination of mechanisms, or an error in your assertions and/or proofs.
I'm still looking for a purpose for this video. A word of advice, and you're free to ignore it, of course: when making videos, state your purpose, why it's important, and then show it without making assumptions.
I don't know why it's so hard for you to grasp the concept that scaffolding alone cannot account for the origin of IC molecular machines whose functions require multiple interacting components, and, this being the case, cooption is required. My purpose here is to show that scaffolding and EFR are not sufficient for generating such IC systems, and thus cooption is required. I will follow this video up with a critique of cooption.
@Genomiques I don't care (and nobody else does either) if scaffolding alone can't generate IC systems. I've already shown a case where cooption isn't required so I'll not bother to repeat it
Showing scaffolding and EFR alone are not sufficient is not the same as showing cooption is required.
imo, you should have started with your video on cooption and simply referred to the paper you quoted in these comments to make your point here. This video is pointless. It addresses a claim no one is making.
"Showing scaffolding and EFR alone are not sufficient is not the same as showing cooption is required."
Other than invoking unknown evolutionary mechanisms, showing that actually does show that cooption is required.
By the way, it IS claimed by a number of critics of irreducible complexity that the Mullerian two-step does offer a solution to the problem of the origin of IC systems.
@Genomiques You have not shown that Mullerian two-step does not offer a solution. I haven't agreed that your argument in this video is valid. I simply didn't want to go around in circles and repeat what I've already said.
Yes, of course more than one protein is required for a great number of functions. This means it fits the definition of IC, but it says nothing about what combinations of mechanisms are involved in its evolution. What did you say that was different than what I said?
You have conceded that many functions require multiple interacting proteins in order to exist. Thus, your general progression of how scaffolding would work, where you start with component A carrying out function X, a function which requires multiple interacting proteins, doesn't work because just one component cannot carry out function X.
@Genomiques Scaffolding can't work with an already IC component A to be part of a more complex IC system? Why not?
Perhaps you're talking about where the very first (simplest) IC system came from only? In that case, wouldn't such a simple system comprised of only two proteins be quite probable by randomness alone? At trillions of trials per second over the entire earth over millions of yrs, it seems inevitable. It's only the very complex systems that the IC argument would have any weight at all.
No, no that' not what I'm saying. I'm saying that your scaffolding scenario starts with one component, A, and then B is added which later becomes necessary. But if A carries out a function that requires MULTIPLE interacting components, then how on earth is A alone supposed to carry out that function? In other words, your scaffolding scenario doesn't work, unless you invoke cooption.
@Genomiques Which is where we were days ago. For the sake of argument, okay, lets assume scaffolding requires cooption to create IC systems (whether or not A is IC btw so your "multiple interacting components" isn't really a factor in the new function). You cannot conclude from this, however, that scaffolding doesn't occur. You've simply established that for IC systems, new functionality may result. This isn't really about mechanisms, however. Yes, new functions are created, IC or not.
I'm not and never did say that scaffolding doesn't occur. But since scaffolding alone cannot result in an IC molecular machine, then cooption is required. And if cooption is shown to have grave problems, then where does this leave us when it comes to explaining the origin of IC molecular machines?
@Genomiques But you haven't shown cooption does have problems, thus the topic of this video is pointless and/or incomplete. Make your video on cooption and state the conclusions of this video as a side note supported by the paper you quoted earlier. I can see how showing cooption is impossible would be important to evolutionary biology. Showing scaffolding may require cooption is a minor issue.
It sounds like you're using cooption as a synonym for a "change in function", and not the mechanism.
I'm not going to show that cooption is impossible, because it clearly isn't. Gene duplication followed by sequence diversification leading to a shift in function has occurred. See, I'm not showing that scaffolding or cooption doesn't happen. I'm showing or going to show that those mechanisms aren't sufficient explanations for the origin of IC molecular machines.
@Genomiques Good luck with that. Many others have tried and failed. I will watch your cooption video and I'm sure we'll have an interesting conversation about it.
Word of advice: "molecular machines" is a subjective concept and only clouds the discussion. I'd suggest you stay away from that term if your intent is to present what you hope will be perceived as science.
Indeed? I'd be interested in watching failed attempts to rebut the cooption scenario as an explanation for IC, here on YouTube - if that's what you meant.
@Genomiques Behe, for one, in Darwin's Black Box and in Edge of Evolution. Both of his extremely similar arguments fail miserably. In DBB, he argues cooption (and any other mechanism actually) can't help lead to IC systems, and in EE he argues it's highly improbable. Perhaps you have a novel approach.
In EofE he mostly talks about the limits of evolution in terms of point mutations etc. If I recall correctly, he didn't spend too much time even discussing irreducible complexity (although he did discuss the IC state of the IFT system). Did he say *why* in both DBB and EofE cooption cannot lead to IC systems (or it's high improbability)?
False. Evidence of precursors that had completely different functions exist. In contrast, there is zero evidence of Behe's theory supports it. Behe also makes assumptions that structures must work well or efficiently in order to be of value to the organism. False, because nature is full of examples of clumsy and imperfect structures that merely get by. Oversimplified with a false premise. This is an unoriginal creationist vlog.
jessydaytime 1 month ago
@jessydaytime
"Evidence of precursors that had completely different functions exist."
But that's not the point of my video (I take it that you DID watch it?). I'm not even saying that IC systems cannot evolve. All I am saying is that scaffolding and Elimination of Functional Redundancy do not offer general solutions to the origin of IC molecular machines. BTW, I'm not a creationist.
Genomiques 1 month ago
Excellent video,well presented and directed,explained thoroughly and scientifically objective.
TheEaglestar1 1 month ago
@TheEaglestar1
Thanks Eagle!
Genomiques 1 month ago
You are forcing component A to have the full function of the bridge, when A does not have the bridge function.
davidmcaba 2 months ago
@davidmcaba
What part of the video are you referring to? Thanks.
Genomiques 2 months ago
@Genomiques 3:45 compared to your original bridge illustration. Component A is not the entire bridge, yet biological component A has the function.
davidmcaba 2 months ago
@davidmcaba
I used the analogy of the bridge to show how scaffolding works, and how, in isolated circumstances, it can generate IC systems. The reason I'm starting with just one component, A, at 3:45, is because I am showing that scaffolding does not offer a general solution to the origin of IC systems that carry out functions which require multiple interacting components.
Genomiques 2 months ago
@Genomiques I understand the point of your argument. I am the false application of the bridge analogy. Component A is only part of the bridge and is not forced to have the "bridge" function, yet you start your argument by forcing A to have the complete function, thus there is the fallacy of equivocation. You are stating that component A of our second model is analogous to the component A of the bridge, but clearly it is not.
davidmcaba 2 months ago
@davidmcaba
The analogy of the bridge is merely to show how scaffolding works to create IC systems. I am not stating that component A of the biological model is analogous to component A of the bridge. Forget the bridge. It is only useful as an explanation of how scaffolding works.
Genomiques 2 months ago
@Genomiques You use the bridge as a demonstration of scaffolding, and then state that its biological equivalent is the ABC block with helper D. You then say, "Thus, for scaffolding to explain the origin of that IC system, we must start with only one component, A, carrying out the function." WHY? You just gave us the analogous physical system that used ABC as the functional unit, and you showed how it was made IC using scaffolding.
davidmcaba 2 months ago
@davidmcaba
I don't state that its biotic equivalent is the ABC block with helper D. When I said "biologically, this can be represented" I meant: "biologically, the concept of scaffolding can be represented with these blocks." Since the ABC complex is already IC, we must explain this system with starting out with just one component, A.
Genomiques 2 months ago
@Genomiques Okay, so you create an alternate representation of bridge ABC. You then show how through one addition and one deletion process, a new IC. None of these systems have one component. You then assert: we must explain this system starting out with just one component. Again, WHY? You just started with a three-component system and through scaffolding, created a new IC system. What is your basis for artificially constraining the system to one component?
davidmcaba 2 months ago
@davidmcaba
If you start with a system that consists of three components, then you've got to also explain the origin of that three-part system. If you take a look at 3:00, you will see that A, B, C, are all necessary to the function, while D is not. This means that A,B, and C form an IC system. So does scaffolding explain the origin of that IC core consisting of components A, B, C? Not if the function is dependent on the interaction of multiple components.
Genomiques 2 months ago
@Genomiques I entirely agree that scaffolding does not explain the origin of the ABC bridge, but three components can easily come together to form a useful function. You are arguing that scaffolding cannot account for larger systems, by making the assumption that we must start with a single component with the full function. This doesn't even take into account how the function changes over time. Proteins often have more than one active site. Some for activity, and some for regulation.
davidmcaba 2 months ago
@davidmcaba
"But three components can easily come together to form a useful function."
Not really, because if they came together all at once to form a useful function, then you need a number of specific, simultaneous mutations occurring. The odds of that happening are next to nil. That's why you don't see any real-time instances of three component molecular machines evolving.
Genomiques 2 months ago
@Genomiques [you need a number of specific, simultaneous mutations occurring] This was the exact blunder Behe made that I was trying to warn you not to make.
HarshColby 2 months ago
@HarshColby
Actually, davidmcaba was suggesting that a three-part IC system could evolve all at once by all three components coming together all at once. And this is highly unlikely because this would mean, by definition, that a number of specific mutations would occur simultaneously. The odds of a three part IC system coming together all at once are next to nil, which is why H. Allen Orr et al. repudiate that view.
Genomiques 2 months ago
@Genomiques Two is still a very small number, and there's no requirement for them to be simultaneous, nor did david say they needed to be. If one non-detrimental mutation occurs, then a million years pass, then another mutation occurs, you'd have this scenario. Any claim of "unlikely" cannot just be asserted. It must be justified. No one doubts it's unlikely to some extent, or we'd see it happening daily. That's different than asserting it's so unlikely that it could not have happened at all.
HarshColby 2 months ago
@HarshColby
Yea but you're assuming that just two mutations would be needed. If we're starting with proteins that carry out entirely different functions, which means that they are usually localized in different subcellular locations, probably more than one mutation would be needed to shift its localization.
Genomiques 2 months ago
@Genomiques Can you provide a link to Orr's statement on this you're referencing? I looked and only found affirmation that IC systems have been observed to evolve via gradual adaptation, citing Muller's work.
HarshColby 2 months ago
@HarshColby
"...it will do no good to suggest that all the required parts of some biochemical pathway popped up simultaneously by mutation. Although this "solution" yields a functioning system in one fell swoop, it's so hopelessly unlikely that no Darwinian takes it seriously. "
- H. Allen Orr, Darwin v. Intelligent Design (Again): The latest attack on evolution is cleverly argued, biologically informed - and wrong.
Genomiques 2 months ago
@Genomiques Orr said Behe is suggesting all the required parts must pop up simultaneously.
Everyone agrees that several mutations "in one fell swoop" is unlikely. That's irrelevant since everyone also agrees mutations need not be simultaneous.
With "two mutations", I was simply referring to the example given. Any number of mutations can happen this way, and since there's no "end goal" in mind, any beneficial combination is allowed, which is far more likely than any 1 specific chain of mutations.
HarshColby 2 months ago
@Genomiques No; it is not impossible for three mutations to occur, and they don't have to be simultaneous. Mutations occur over time, and neutral mutations may later become useful. Please note in your example of the bridge that A and C are not needed, only B, but later, A and C are essential with D, and B is no longer in the picture.
davidmcaba 2 months ago
@davidmcaba
"No, it's not impossible for three mutations to occur."
Of course, I never claimed that o.o
But, if I understand you correctly, you are suggesting that system ABC could have arisen in one fell swoop, with all three components coming together, forming a novel function. And that's unlikely.
Genomiques 2 months ago
@Genomiques Really, how unlikely? Would you say it's unlikely for me to toss a quarter and receive a head three times in a row?
davidmcaba 2 months ago
@davidmcaba
No, it's not all that unlikely for you to toss a quarter and receive a head three times in a row. The odds of that happening are 1 in 2^3, or 1/8. Quite likely, actually. This is not the same odds for three specific mutations to occur, giving rise to a novel function.
Genomiques 2 months ago
@Genomiques Great, now how unlikely is it for three components to come together to form a function?
Also, please note that you've already asserted that it could happen with the bridge example. ABC are three components, to which you added D and subtracted B, and now you have a three-component IC system.
davidmcaba 2 months ago
@davidmcaba
It depends on the components, and where the original components are localized in the cell. If the components are localized in different sublocations in the cell, then almost certainly more than one mutation will have to occur to each component to bring them to a new cellular location.
Genomiques 2 months ago
@davidmcaba
"Also, please note..."
Yea but with the bridge example we're already starting with three components.
Genomiques 2 months ago
@Genomiques Also note, in the original idea of the bridge, none of the parts are forming a bridge. They are simply three parts lined up. The addition of D and subtraction of B creates the bridge function.
davidmcaba 2 months ago
@davidmcaba
"Also note..."
Actually, the parts do form a bridge. Look again. They don't form an irreducibly complex bridge, but they do form a bridge nonetheless.
Genomiques 2 months ago
@Genomiques No, the original idea of a bridge forming from scaffolding has three parts that are not a bridge. The addition of D and subtraction of B forms the bridge. In your modified example, you have started with a bridge, and modified it to form another bridge.
The function of the bridge is to arise from the process, not be assumed at the start.
davidmcaba 2 months ago
@davidmcaba
"No, the original idea of a bridge forming scaffolding has three parts that are not a bridge..."
I don't see how this is important at all to my illustration of how a bridge can become irreducibly complex through scaffolding.
Genomiques 2 months ago
@Genomiques Because you cheat the example by giving the system the function from the beginning. The real example show how the bridge function arises from the scaffolding process. This is the heart of the issue. You say scaffolding cannot produce multi-component IC systems, yet this is precisely what the bridge example demonstrates.
davidmcaba 2 months ago
@davidmcaba
"This is the heart of the issue."
No, it's not, 'cause the only reason I use the bridge is to demonstrate how scaffolding works to create IC systems. Scaffolding cannot produce multi-component IC molecular machines without the invocation of cooption, if those molecular machines carry out functions that require multiple interacting components in order to exist.
Genomiques 2 months ago
@Genomiques You are simply stating your thesis. I have already shown two errors in your presentation. 1) You incorrectly present bridge scaffolding by giving the bridge function to the initial ABC system, when it is supposed to arise from the ADC system that arises from the ABC system through scaffolding. 2) You continue this error by false attributing the full function to a single component, which is the cornerstone of your argument.
davidmcaba 2 months ago
@davidmcaba
Yea but:
"A clear example of the Mullerian two-step [which is essentially scaffolding] is given by a stone bridge. Consider a crude 'precursor bridge' made of three stones. This bridge spans the area needed to be crossed and is thus functional. For step one of the Mullerian two-step, a part is added: a flat stone on top, covering all precursor stones. Whether this improves the functionality of the bridge is irrelevant..."
"Why Behe's 'Irreducible Complexity' is Silly," TalkOrigins
Genomiques 2 months ago
@davidmcaba
As you can see from the quoted article (written by Dr. Douglas Theobald), I do not misrepresent bridge scaffolding.
Genomiques 2 months ago
@davidmcaba
Finally, I have already said many times that I am ONLY using the bridge example as an example of how scaffolding works. There are many biological functions which can only function through the interaction of multiple components. Such systems cannot arise through pure scaffolding because you'd have to start with one component, but one component cannot carry out the function. If you invoke changes of function, then you're using cooption as your explanation, not scaffolding.
Genomiques 2 months ago
@davidmcaba
We must start with a single component because otherwise you're starting with multiple components which all fortuitously came together, which is highly improbable - evolutionary biologist H. Allen Orr acknowledges that, e.g.
"This doesn't even take into account how the function changes over time. Proteins often have more than one active site."
And the relevance of this statement is where? o.o
Genomiques 2 months ago
@davidmcaba
If you still want to use the bridge as an analogy, then you will notice that the bridge starts out with three components in the first place. If the bridge was a biological entity, then its evolution would have to occur step-by-step, starting with just one component imparting a beneficial function to the organism.
Genomiques 2 months ago
@davidmcaba
In short, using the bridge as an analogy was just to show how scaffolding works.
Genomiques 2 months ago
Okay up to 3:25, where you started to make unsupported assertions. After 3:25, your argument falls apart.
HarshColby 3 months ago
@HarshColby
But how did it fall apart? Your criticism was that he started making unsupported claims that fell apart. But you haven't substantated your claim that these arguments made in the video (after 3:25) actually did fall apart.
But perhaps you can list some reasons why you believe that these claims fall apart after 3:25?
tubewatch59 3 months ago
@HarshColby
At 3:25:
"However, while scaffolding may explain the origin of some IC systems, it fails as an explanation for the origin of IC systems whose function depends on the interaction of multiple gene products."
How is this an unsupported assumption? At 4:50 I present a small sample of molecular machines that carry out functions which require multiple gene products. This is not an unsupported assumption. So, please tell me, where are my unsupported assumptions after 3:25?
Genomiques 3 months ago
@Genomiques An example of one place where you, personally, can't think of how something may have happened, doesn't show it's impossible. Perhaps you're just not clever enough to figure it out. (Perhaps no one is, but that doesn't make it impossible or even improbable.) As it turns out however, biologists, (the people that understand this the best), have no problem whatsoever seeing how it happens, for this example.
Keep in mind that the multiple genes don't have to have evolved at the same time.
HarshColby 3 months ago
@HarshColby
"An example of one place where you, personally, can't think of how something may have happened, doesn't show it's impossible."
Yea but you're ignoring my question. Where exactly does my video break down and how does it? What I am doing here is showing how scaffolding and elimination of functional redundancy doesn't offer a general solution to the origin of IC molecular machines. This isn't lack of imagination on my part, otherwise you could simply respond to the actual arguments.
Genomiques 3 months ago
@HarshColby
"Perhaps you're just not clever enough to figure it out."
Figure what out? Again, I am not making an argument from imagination here. My arguments in this video are supported by real biology. The point of this video is not that Darwinian mechanisms cannot explain the origin of IC molecular machines. The point is that the specific pathways of scaffolding and Elimination of Functional Redundancy don't work. Respond to those points, rather than go after a red herring. Thanks.
Genomiques 3 months ago
@HarshColby
"Keep in mind that the multiple genes don't have to have evolved at the same time."
Duh. As if I didn't know that.
Genomiques 3 months ago
@Genomiques [Duh] Well, Behe doesn't know that, so I'm not assuming anything.
What "real biology" is your video using? Yes, you assert scaffolding doesn't work, but you haven't supported it with biology. You supported it with assertions that it doesn't work.
@3:25 You support the assertion "fails...whose function depends on...multiple genes" with an argument based on the assertion "must start with one component".
@3:44: What "real biology" supports "we must start with only one component"?
HarshColby 3 months ago
@HarshColby
I don't think you quite understand the video. In the scaffolding scenario, components A + B + C are necessary to the molecular machine, while D is helpful but not necessary. D then becomes a necessary component as the system evolves. But this scenario already starts with an IC system: A + B + C, so how does scaffolding explain the origin of that IC core? (continued)
Genomiques 3 months ago
@Genomiques Yes. I understand that just fine. It's irrelevant. You're setting up a scenario which you can easily refute, while ignoring the point of the argument. If you're just going to say a+b+c is IC, then make your scenario discuss a+b+c. Adding D just sets it up so you don't have to address the point. For your argument to make any sense, you'd have to assume that ALL configurations a+b+c are IC. They're not, of course, so why make it a requirement? All systems a+b are not IC.
HarshColby 3 months ago
@HarshColby
"If you're just going to say a+b+c is IC, then make your scenario discuss a+b+c..."
Gee whiz. I did exactly that. Did you watch the video? See 3:43 through 4:30. You didn't SERIOUSLY think that my refutation of scaffolding as a general solution to IC is simply "we're already starting with an IC system, so scaffolding doesn't work." No, my refutation is more elaborate than that.
Genomiques 3 months ago
@HarshColby
So, in the scaffolding scenario, how do we evolve an IC system that requires components A + B + C? We would start with one component, A, which later becomes necessary to the function. If we start with two components, say, A + B, then that system is already irreducibly complex, and so scaffolding must explain the origin of *that* IC system (continued).
Genomiques 3 months ago
@HarshColby
If, on the other hand, A + B are helpful, but not necessary components - the A+B system not being IC at first, then - we run into the problem that there are a whole bunch of biological functions out there that demand the interaction of multiple gene products; i.e., A+B would be necessary. And so scaffolding would have to account for the origin of that IC system. See the problem? Try to visualize what I'm saying here and then it may be clear.
Genomiques 3 months ago
@Genomiques And the problem with "multiple gene products" is what? Why couldn't A and B be present but not necessary? Then a+b+c become present and performs a new function, which was not preformed by A and B alone? a+b+c thus become required for the new function, but not required for the survival of the organism.
HarshColby 3 months ago
@HarshColby
"And the problem with 'multiple gene products' is what? Why couldn't A and B be present but not necessary?"
Here's why: if we're using scaffolding to explain the IC state of molecular machines whose very functions require the interaction of multiple gene products - I present a small sample of such machines in the video - then A+B must be necessary because the function REQUIRES interaction of multiple gene products (continued).
Genomiques 3 months ago
@Genomiques You're overly complicating the explanation by bringing up A+B+C+D. Your stated initial condition is that A+B are required for function X. Therefore A+B is IC with respect to function X. Then you simply assert that A+B couldn't have been placed there via a scaffold @4:27.
@4:27 you seem to be assuming that function (A) and function (A+B) are identical. If function (A+B) can't be carried out by A alone, then it's irrelevant to your argument and you shouldn't need to bring up A at all.
HarshColby 3 months ago
@HarshColby
"...you seem to be assuming that function (A) and function (A+B) are identical."
Yea because otherwise we'd talking about cooption, not scaffolding. In a purely scaffolding scenario, no change of function would take place: that's called cooption. This video does not address cooption, and so it doesn't invoke cooption.
Genomiques 3 months ago
@HarshColby
"If function (A+B)can't be carried out by A alone, then it's irrelevant to your argument..."
No, that's the POINT of my argument. The POINT of my argument is that scaffolding doesn't explain the origin of IC molecular machines that carry out functions which, by their very nature, require the interactions of multiple components. Thus, pure scaffolding cannot explain the origin of such IC molecular machines - and there are a fairly large number of them.
Genomiques 3 months ago
@Genomiques Now you're just making claims based on semantics, not logical thought or science. It doesn't matter that scaffolding exists along side other mechanisms. IC systems still evolve, and scaffolding is heavily involved. You seem to have just eliminated any purpose to your video.
Your original comment was "this video explaining why evolutionary pathways have a hard time explaining the origin of IC molecular machines". This video doesn't show anything of the kind.
HarshColby 3 months ago
@HarshColby
No, my arguments have nothing to do with semantics. The point of this video is that pure Scaffolding and pure Elimination of Functional Redundancy cannot feasibly offer a general solution to the origin of IC molecular machines.
"It doesn't matter that scaffolding exists along side other mechanisms."
Oh yes it does, 'cause if you're going to be invoking cooption then why invoke scaffolding? It's superfluous to do that (continued).
Genomiques 3 months ago
@HarshColby
"You seem to have just eliminated any purpose to your video."
The purpose:
To explain why scaffolding and Elimination of Functional Redundancy do not sufficiently explain the origin of IC molecular machines. Cooption would have to be invoked, and if you invoke cooption along side scaffolding, then why invoke scaffolding? You're not being logical now, are you?
Genomiques 3 months ago
@Genomiques Then you failed. Your argument is incoherent. Your explanation here in the comments section hasn't clarified your position.
A to A+C to A+C+B to A+B is quite sufficient. That's scaffolding without a requirement for cooption. Plus, even if cooption is required, that doesn't mean scaffolding doesn't happen and/or isn't involved.
HarshColby 2 months ago
@HarshColby
"Then you failed."
Not really.
"A to A+C to A+C+B to A+B is quite sufficient."
I've already responded to this line of thought many times, yet you are still unable to get it. If A to A+C share the same function, then this does NOT work if we're talking about the origin of an IC molecular machine whose function REQUIRES the interaction of multiple components. I.e., that function could not be carried out just by A. (continued)
Genomiques 2 months ago
@HarshColby
Now, if A and A+C do not carry out the same function, then you're invoking cooption, so using scaffolding alongside cooption is superfluous. So your comment "that's scaffolding without a requirement for cooption" has been thoroughly responded to: scaffolding, without cooption, cannot explain the origin of IC molecular machines - and read this carefully - that carry out functions which, by their very nature, require the interaction of multiple components. (continued)
Genomiques 2 months ago
@HarshColby
And that is the point of my video: that the scaffolding pathway is does not explain the origin of that large number of molecular machines that carry out functions which require the interaction of multiple components. The function of bacterial motility through Brownian motion cannot be accomplished with just one component, A. So starting out with A, then A+C does not work. And if a shift of function occurs, you're invoking cooption.
Genomiques 2 months ago
@HarshColby
Which means, again, that your statement that "that's scaffolding without a requirement for cooption" is incorrect with regards to the core argument in this video.
"Plus, even if cooption is required, that doesn't mean scaffolding doesn't happen and/or isn't involved."
Quite true, but if cooption is required, then invoking scaffolding is simply superfluous and doesn't by itself explain the origin of the IC system. Which means that cooption is the only viable evolutionary route.
Genomiques 2 months ago
@Genomiques If cooption occurs, that means scaffolding is superfluous? Do you think they're mutually exclusive in the universe? Cooption disproves scaffolding? What an odd thing to assert.
HarshColby 2 months ago
@HarshColby
"If cooption occurs, that means scaffolding is superfluous?"
If cooption is REQUIRED for the origin of an IC molecular machine, then invoking scaffolding isn't necessary. The two are obviously not mutually exclusive, but that's not the point. The point is that just because scaffolding plays a role in modifying an IC system that was evolved by cooption doesn't mean that scaffolding is a feasible explanation for the origin of IC molecular machines (continued).
Genomiques 2 months ago
@HarshColby
You still don't seem to be getting the point of this video.
Just answer this simple question, with a "yes" or "no" answer, and provide explanations if the answer is "yes."
The question is:
Is scaffolding alone a feasible evolutionary pathway for the origin of IC molecular machines whose functions require the interaction of multiple components?
I will await your answer.
Genomiques 2 months ago
@Genomiques Quite right. I see no point to your video.
Who cares if scaffolding alone works? I don't. Biologists don't. You shouldn't. It's an irrelevant point. Evolution of IC systems happens regardless of the answer, which is why it's an irrelevant question.
Yes, scaffolding alone is a feasible evolutionary pathway for any system, IC or not. I gave you the general progression already. There's no indication of cooption in my statement. Cooption may or may not be present.
HarshColby 2 months ago
@HarshColby
"Who cares if scaffolding alone works. I don't [you're no biologist]. Biologists don't [oh yes they do]."
If scaffolding alone doesn't work, and if Elimination of Functional Redundancy alone doesn't work, and if cooption alone doesn't work, then there is no viable evolutionary pathway for the origin of IC molecular machines. Your inability to grasp this concept is, well, plain absurd o.o
Genomiques 2 months ago
@HarshColby
"Evolution of IC systems happens regardless of the answer, which is why it's an irrelevant question."
Indeed? Then I should like to know how IC molecular machines evolved through non-teleological mechanisms, without your invoking scaffolding, Elimination of Functional Redundancy, or cooption. If you don't provide a mechanism, then you must concede that if we eliminate the viability of those three pathways then Darwinian evolution does have a hard time explaining IC machines.
Genomiques 2 months ago
@HarshColby
"Yes, scaffolding alone is a feasible evolutionary pathway for any system, IC or not. I gave you the general progression already."
And I have soundly thrashed your 'general progression' so thoroughly that your repeating of it is getting increasingly monotonous. (continued)
Genomiques 2 months ago
@HarshColby
Here's why your general progression for scaffolding, in the absence of cooption, doesn't work for the origin of that large number of IC molecular machines whose functions require the interaction of multiple components:
If the FUNCTIONS of those IC molecular machines REQUIRE multiple components, then starting with component A carrying out the function is impossible since the function cannot work with just one component like A. (continued)
Genomiques 2 months ago
@Genomiques It doesn't matter how many components are required. That's where I began by saying you need to stop assuming things. Scaffolds can be as complex or as simple as you'd like. Scaffolding still happens.
You haven't "roundly thrashed" anything. You've simply restated you initial assumptions as if they're correct. It was wrong the first time you asserted it, and it's still wrong now.
A+B may perform the exact same function as A: no cooption. A+B could be a brand new function: no cooption.
HarshColby 2 months ago
@HarshColby
"It doesn't matter how many components are required."
Oh yes it does. If an IC molecular machine carries out a function that requires the interaction of multiple components, then your scaffolding scenario starting out just with one component, A, doesn't work *because the function cannot exist with just one component.* And IF you say that component A isn't carrying out the same function as A+B, then you are invoking cooption, which means pure scaffolding doesn't work.
Genomiques 2 months ago
@HarshColby
"That's where I began by saying you need to stop assuming things."
The only thing I am assuming - and this assumption is backed up by a number of clues - is that you lack a college level education in any biological discipline.
"Scaffolding still happens."
I never denied that. However, as this video argues, pure scaffolding does not offer a general solution to the *origin* of IC molecular machines.
Genomiques 2 months ago
@HarshColby
"A+B may perform the exact same function as A: no cooption."
Of course, this does NOT work because if A+B performs the same function as A, and if that function by its very nature can only exist by the interaction of MULTIPLE components, then a single component, A, by definition, cannot carry out that function. Your problem is that your starting out with only one component, but many biotic functions can only exist through the interaction of several componenets. Try again o.o
Genomiques 2 months ago
@Genomiques
components*
Genomiques 2 months ago
@HarshColby
And of course, that's the point of this video: that pure scaffolding cannot feasibly explain the origin of that fairly large number of IC molecular machines which carry out functions which require the interaction of several components. That is THE point of this video. You have been unable to refute that point, I'm afraid.
Genomiques 2 months ago
@Genomiques If your point is restricted to what you just said, then my overall response is "so what"? The evolution of IC systems is not claimed by anyone to rely solely on scaffolding. I've refuted it. You just missed the point because you're still operating under the mistaken assumption that your claims are accurate.
HarshColby 2 months ago
@HarshColby
"If your point is restricted to what you just said, then my overall response is 'so what'?"
My point IS restricted to what functions which require the interaction of multiple components in order to exist, and your realization only now that this is my point is a bit absurd o.o
Since such functions cannot be evolved via scaffolding and Elimination of Func. Redundancy, then the only viable route is cooption, correct?
Genomiques 2 months ago
@Genomiques [Since such functions cannot be evolved via scaffolding and Elimination of Func. Redundancy, then the only viable route is cooption, correct?] Wrong. Evolution of a particular function can involve any or all of those. Those words and concepts exist because they've been observed to occur. To claim they don't occur is absurd, and I said so in the beginning.
HarshColby 2 months ago
@HarshColby
"Wrong. Evolution of a particular function can involve any or all of those."
We're not talking about the plain ole' evolution any ole' function. We're discussing the origin of IC molecular machines which carry out functions that require multiple interacting functions in order to exist. Pure scaffolding cannot explain the origin of such systems, and so cooption must be invoked. In short, in the absence of cooption, such functions cannot evolve.
Genomiques 2 months ago
@Genomiques There's no established difference between the evolution of IC systems and non-IC systems. If you disagree, then explain how they differ. (Don't just define it. I already know that "if you remove one part" definition that's meaningless.)
HarshColby 2 months ago
@HarshColby
"There's no established difference between the evolution of IC systems and non-IC systems."
Actually, when it comes to molecular machines, there is a difference. If a molecular machine's function is not IC, then it could have evolved through gradual improvement upon one, same function. However, this doesn't work if a molecular machine is IC: you must propose a different pathway to account for the IC state of the system.
Genomiques 2 months ago
@Genomiques Oh? How so? In what way can an IC system not evolve in a gradual step-by-step way using the very mechanisms you've outlined in your video? To avoid your assertions we've already discussed (to no avail), what if all these mechanisms are involved in all evolutionary processes? You haven't claimed that scaffolding plus cooption can't produce IC systems, have you? (If you did, you're wrong, of course.)
HarshColby 2 months ago
@HarshColby
"In what way can an IC system not evolve in a gradual step-by-step way using the very mechanisms you've in your video?...what if all these mechanisms are involved?"
I've demonstrated that scaffolding alone does not offer a general solution to the origin of IC machines, and so if scaffolding alone doesn't work then you have to invoke cooption. Which means that cooption + any optional mechanisms is the only viable evolutionary pathway for the origin of such systems.
Genomiques 2 months ago
@HarshColby
Remember, the point of this video is this: *scaffolding alone does not explain the origin of IC molecular machines which carry out functions that require multiple interacting components in order to exist.* Do you, or do you not, agree with that statement?
Genomiques 2 months ago
@Genomiques And remember I've already opined the point of this video is meaningless.
No. I don't agree. Scaffolding is involved and you haven't shown otherwise. You've claimed scaffolding alone does not produce IC evolution (wtf is a machine in this context anyway?). You haven't shown, and in fact have stated, that scaffolding IS involved in evolution.
[Which means that cooption + any optional mechanisms is the only viable evolutionary pathway ] And what would that imply?
You didn't answer my Q.
HarshColby 2 months ago
@HarshColby
"And remember..."
Yea but it's not meaningless, because if scaffolding and EFR alone cannot explain the origin of such IC machines, then you must invoke cooption. Which means that cooption is the only viable pathway for the origin of such systems.
Genomiques 2 months ago
@HarshColby
So you do not agree that *scaffolding alone does not explain the origin of IC molecular machines which carry out functions that require multiple interacting component in order to exist*? Then please explain how, in the scaffolding scenario, you can start with one component, A, carrying out Function X which requires multiple components in order to exist?
Genomiques 2 months ago
@Genomiques [explain how, in the scaffolding scenario, you can start with one component, A, carrying out Function X which requires multiple components in order to exist?] I already have, but... here's one:
Protein A (to clarify what "A" is) performs no function whatsoever by itself. Protein B performs no function whatsoever by itself. But A+B performs function X. No cooption involved. (No scaffolding involved either, but your question was about how the original two components can have existed.)
HarshColby 2 months ago
@HarshColby
"...but...here's one:"
I compliment you on your imagination but I am disappointed in your ignoring of natural selection. If proteins A and B performs no functions, then random mutations will hit those genes, and natural selection will probably eliminate them from the gene pool. But assuming this doesn't happen: my question actually was not how the original two components could have existed.
Genomiques 2 months ago
@Genomiques [then random mutations will hit those genes, and natural selection will probably eliminate them from the gene pool.] Why would RM eliminate those genes? The error rate in gene reproduction is 10^(-8), which means it'd take millions of generations before it's likely to be eliminated. Within the time span of those generations, the other DNA sequence mutation would be relatively likely. Keep in mind that random mutation happens trillions of times a second throughout a large population.
HarshColby 2 months ago
@HarshColby
Random mutations would hit those genes, destroying their sequence identity, which means that they probably won't be able to carry out any future function. On top of that, it's natural selection that would eliminate functionless genes from the gene pool, in bacteria anyway, since with unicellular organisms their is a cost associated with keeping genes that carry out no function, especially if those genes are translated.
Genomiques 2 months ago
@Genomiques
there*
Genomiques 2 months ago
@HarshColby
My question was how only one component, A, can carry out a function that REQUIRES *multiple* components in order to exist. That IS the question. That's why my question is relevant to scaffolding, while the scenario you just outlined really isn't.
Genomiques 2 months ago
@HarshColby
Scaffolding is involved in evolution. But scaffolding does not explain the ORIGIN of IC molecular machines whose functions require the interaction of multiple component. Scaffolding can modify that system, but it does not explain the ORIGIN of that system. Simple concept, right?
Kindly repeat your question. Thanks.
Genomiques 2 months ago
@HarshColby
"And what would that imply?"
That scaffolding and EFR alone are not adequate pathways for the origin of IC machines, which means you MUST rely on cooption.
Genomiques 2 months ago
@Genomiques [That scaff. and EFR alone are not adequate...for the origin of IC machines, which means ...cooption.] And, in turn, what would that imply?
Answer my question about the difference between the evolution of IC systems and non-IC systems. You can't even define an IC system in terms of mechanisms. You can only define it (as Behe did) as a system where taking away one part changes the function. That's true of virtually ALL systems, biological, mechanical or otherwise, is it not?
HarshColby 2 months ago
@HarshColby
"Answer my question..."
An IC system could not have evolved through gradual improvement of one function. For example, consider a system that I would not consider IC: the giraffe's neck. The giraffe's neck evolved through gradual improvement upon the length of the neck. Now, if a system is IC, then the pathway of gradual improvement of one function doesn't work because elimination of a part results in a different function, meaning that evolution must work on different functions.
Genomiques 2 months ago
@Genomiques [An IC system could not have evolved through gradual improvement of one function. ] Not true. But so what? Say I grant you this. Now what? Say I also grant that in an IC system requires that an added protein that changes the function (cooption). Then what?
HarshColby 2 months ago
@HarshColby
Then what? Well, what if, upon further analysis, the cooption scenario also breaks down? Then what? You don't have a viable evolutionary pathway for the evolution of IC molecular machines.
Genomiques 2 months ago
@Genomiques [what if, upon further analysis, the cooption scenario also breaks down] Why? Are you likely to present such an argument? (<== bad attempt at Douglas Adams humor). If you could show that no combination of scaff, EFR, and cooption works, then you're left with all the other mechanisms which you haven't included in your argument. Any of these unknown mechanisms could be the actual mechanism used. It's nearly impossible to prove a negative, so your work is cut out for you.
HarshColby 2 months ago
@HarshColby
"Are you likely to present such an argument?"
You shall see what you shall see.
"Then you're left with all the other mechanisms which you haven't included in your argument..."
By "other mechanisms," I suppose you mean unknown mechanisms which you think they must be there? They may be there, but since no one knows where we might find these guys, non-teleology is no longer the default explanation.
Genomiques 2 months ago
@Genomiques [You shall see what you shall see] Then you should have started with that argument. Presenting a video without a meaningful purpose isn't helping anyone. The main problem with your video here, aside from a lack of obvious purpose, is that it's not even making a convincing argument for the elimination of scaffolding or EFR. You've simply presented the scenarios you feel you can shoot down (yet you failed to do so), and you've ignored the fact that these mechanisms are know to occur.
HarshColby 2 months ago
@HarshColby
"..and you've ignored the fact that these mechanisms are known to occur..."
You seem to have a hard time grasping the concept that even though these mechanisms occur doesn't mean that they explain the origin of all IC molecular machines. For example, neither EFR nor scaffolding alone could explain the origin of the bacterial flagellum.
Genomiques 2 months ago
@Genomiques [ the concept that even though these mechanisms occur doesn't mean that they explain the origin of all IC molecular machines] Using another creationist argument? I've asked, but have not received, your explanation of how you think the mechanisms of IC evolution differs from any other evolution. Biologists (the people that understand this stuff the best) see no difference. It's creationists that need to ignore observation and invent new terms, like ID and IC to confuse people.
HarshColby 2 months ago
@HarshColby
I have answered your question, and so have the biologists:
See Thornhill, R. and Ussery, D.W. 2000. "A Classification of Possible Routes in Darwinian Evolution." Journal of Theoretical Biology.
Read their paper thoroughly and your question may be answered.
Genomiques 2 months ago
@Genomiques [For example, neither EFR nor scaffolding alone could explain the origin of the bacterial flagellum.] Biologists don't say any one mechanism alone does explain the BF. You're arguing against a claim no one makes. Here's one detailed description of how standard evolutionary biology can be used to explain the BF:
talkdesignDOTorg/faqs/flagellum.html
[asserting unknown evolutionary mechanisms] Only known mechanisms are asserted. We leave unknown mechanisms to theists :)
HarshColby 2 months ago
@HarshColby
"Biologists don't say any one mechanism alone explains the BF..."
Actually, cooption is the only mechanism used to explain the IC core of the bacterial flagellum. Regarding your link, I could in fact show you exactly where that pathway breaks down (well, it breaks down at the beginning), but I can hardly do so in 500 characters.
Genomiques 2 months ago
@Genomiques Btw, I'm not asking "and what would that imply" to be pedantic. I'm trying to get to the root cause of your belief that your video discusses a meaningful point. To cut to the chase, assume I grant you all your claims. Why is any of this important? What end message are you going for, and why is it important to our understanding of evolution? Say, for the sake of argument, that scaff, EFR, and cooption are all required for all evolution and no evolution could occur without cooption.
HarshColby 2 months ago
@HarshColby
"Why is any of this important?"
Firstly, keep in mind that I am discussing this from the angle of molecular machines. You say "and no evolution could occur..." Well, I'm not attacking the theory of evolution at all. I'm analyzing the concept that IC molecular machines evolved through scaffolding, EFR, and cooption. (continued)
Genomiques 2 months ago
@HarshColby
So, to cut to the chase, if the evolution of IC molecular machines could only occur through cooption, then if we find cooption ALSO to be an inadequate explanation for the origin of those machines, then there's really no satisfactory non-teleological evolutionary explanation for the origin of those machines. This video doesn't discuss cooption because it's a topic all of its own.
Genomiques 2 months ago
@Genomiques Your examples specifically rule out any discussion of cooption+scaffolding+EFR, so you still haven't shown that evolution of IC systems is impossible. You've only shown (if you were to show) that more than one mechanism is involved. Also, you've ruled out any discussion of any other mechanisms that may be involved of which you just aren't familiar. All you've done is arrived at the basic teleological argument for God, which is essentially an just an argument from ignorance.
HarshColby 2 months ago
@HarshColby
My discussion only shows that scaffolding and EFR can only explain an IC molecular machine is cooption is involved. That was the point of this video, and I will discuss cooption in another. If we rule out the viability of cooption, then cooption+scaffolding+EFR doesn't work either, because the viability of all three pathways has been eliminated.
Genomiques 2 months ago
@Genomiques Natural selection would only eliminate detrimental sequences, not neutral ones. Most mutations are neutral, neither beneficial or detrimental, which is why "junk DNA" stick around for so long. Look at the largest genome, the amoeba dubia. If you are right, then the DNA sequences would have long since disappeared. Why didn't they?
HarshColby 2 months ago
@HarshColby
I get the feeling that we're going off on an unimportant tangent. But anyhew, the amoeba's genome is mostly untranslated nucleotide sequences, which means there isn't a negative cost associated with a large genome. But if all those sequences were translated into amino acid sequences, then there would definitely be a metabolic cost, especially for unicellular organisms.
Genomiques 2 months ago
@HarshColby
Feel free to list another evolutionary mechanism other than cooption, scaffolding, and EFR that might explain the origin of IC molecular machines. And I didn't mention any gods or deities - you're automatically assuming I'm a theist, it seems, never considering the possibility that I may actually be an agnostic or an atheist or one of those who simply don't care if gods exist or not. Also, IC in itself is not positive evidence for teleology.
Genomiques 2 months ago
@Genomiques [Feel free to list another evolutionary mechanism other than cooption, scaffolding, and EFR] And what if I can't? Does that mean there aren't any? For your argument to prove anything, you'd have to know for sure that there aren't any. "Because I'm not smart enough to think of one" is not a valid argument. You'd have to show, there are, in fact, no others. You haven't shown this.
You mentioned teleology, which is a standard argument for God. I didn't assume anything.
HarshColby 2 months ago
@HarshColby
Right, and I suppose if we found a metallic pyramid-shaped object floating in space it would be illogical to conclude that it was designed because there might be non-telic mechanisms that we can't think of that would explain its origin?
"You mentioned teleology, which is a standard argument for God."
I think I've explained this to you before. By "teleology" I mean exactly what it means: a purposeful, goal-oriented mechanism. The word "god" isn't even part of the definition.
Genomiques 2 months ago
@Genomiques [teleology] Then my mistake. Both IC and the teleological argument are very common creationist arguments for the existence of God. When you use the terms, you must expect that people will conclude that your end goal is to disprove evolution and posit a God is required. Especially when you've not been forthcoming with why you're going down this road in the first place.
HarshColby 2 months ago
@HarshColby
"Especially when you've not been forthcoming with why you're going down this road in the first place."
I'm doing my best to approach the discussion of biological origins with as much objectivity as I can. And so I readily admit that, contrary to what many creationists say, IC in itself is not a positive indicator of intelligence. So too, I often wonder why non-teleologists like yourself don't find the existence of a genetic code, e.g., at least SUSPICIOUS of intelligence.
Genomiques 2 months ago
@Genomiques [IC in itself is not a positive indicator of intelligence] Finally something we can agree on.
I don't find the genetic code indicates an intelligence for two main reasons:
1. I understand how the code would naturally develop via RM and NS.
2. An intelligence which did not develop in a way consistent with biology and physics would need an insurmountable amount of explanation ... an explanation much more complicated than the evolution of systems you're trying to explain.
HarshColby 2 months ago
@HarshColby
"I understand how the code would naturally develop via RM and NS."
Keep in mind that just because something *can* evolve through non-intelligent mechanisms does *not* necessarily reflect its true history. Just saying.
"An intelligence which did not develop in a way consistent with biology and physics..."
You are, of course, assuming that an intelligence would not have developed in a way consistent with biology and physics.
Genomiques 2 months ago
@Genomiques [Keep in mind that just because something *can* evolve through non-intelligent mechanisms does *not* necessarily reflect its true history] And again, we can agree. Yet, positing convoluted unknown and untestable mechanisms when known physics and biology provide the mechanisms, seems unnecessary. Perhaps rainbows *are* created by supernatural or unknown mechanisms, but that's no reason to ignore optics.
HarshColby 2 months ago
@HarshColby
Untestable mechanisms? The front-loading hypothesis is very testable, and it is inherently teleological.
Genomiques 2 months ago
@Genomiques FL is testable? Not in the least. Your video claims it's testable, but didn't bother to show this is true.
You can't show what this video purports to show, so I doubt very much that you can show exactly where my linked article breaks down.
Your linked paper says that evolution of IC systems is possible. How does that support your claim? (It doesn't define IC any differently than Behe did however. My question is how you'd identify an IC system, which the paper states is unclear.)
HarshColby 2 months ago
@HarshColby
"FL is testable? Not in the least."
I'll reserve the particular discussion for another day, but of course, any one with any real training in biology could see how we could test that hypothesis.
"You can't show what this video purports to show..."
Oh yes I can, and I have. You haven't refuted anything. Your inability to grasp basic concepts isn't a reflection of my intelligence but yours.
Genomiques 2 months ago
@HarshColby
You seem entirely incapable of understanding, for example, that one component, A, cannot carry out a function that requires multiple interacting components to exist. This is a simple concept, but you can't get it, can you?
"Your linked paper says that evolution of IC systems is possible."
Of course, I never denied that. The paper also explains why the evolution of IC systems require different mechanisms than the evolution of nonIC systems. Your comprehension skills aren't that bad?
Genomiques 2 months ago
@Genomiques No. It talks about the same mechanisms. What's new?
Don't start with the insults or I'll leave you with your delusions.
HarshColby 2 months ago
@HarshColby
"No. It talks about the same mechanisms."
It *talks* about Darwinian mechanisms, but it also says that serial direct Darwinian evolution - change along a single axis - cannot generate irreducibly complex systems.
Genomiques 2 months ago
@Genomiques The question was how you can tell what an IC system is in terms of mechanisms. The answer is there is no difference in the mechanisms. The same mechanisms which result in IC systems are also used in all evolution. The mechanisms aren't any different, although the paper does say some mechanisms by themselves won't yield IC systems. This is not the same as your claim (that no mechanisms exist which will yield IC systems). This paper refutes your claims, so I question why you linked it.
HarshColby 2 months ago
@HarshColby
Yea but:
Although all mechanisms used in the evolution of IC systems can also be used in the evolution of non-IC systems, the reverse is not true: all mechanisms used in the evolution of non-IC systems cannot all generate IC systems. Please tell me exactly where I claimed that no mechanisms will yield IC systems.
Genomiques 2 months ago
@Genomiques Sure. That's fine. Some mechanisms by themselves wouldn't result in IC systems. So if you agree that IC systems can evolve, then I'm still missing the point you're trying to make. If your only point is that more than one mechanism is involved, and no one is making claims that only one mechanism is involved, then we're back to this video having no point. Who cares if cooption is required along with scaffolding, ERF or other mechanisms? Your answer was that you'll make another video.
HarshColby 2 months ago
@HarshColby
Well, if cooption is required to generated IC molecular machines that carry out functions which require multiple interacting components, then if we find that cooption also fails as a general solution to the origin of IC molecular machines, we must conclude that there are no known, robust, non-teleological explanations for the origin of IC molecular machines.
Genomiques 2 months ago
@Genomiques
to generate*
Genomiques 2 months ago
@Genomiques You were wise to add "known" in your conclusion. So, if you could show cooption was both required and inadequate (two tings you have yet to show), then you're left with some unknown (to you) mechanism, a combination of mechanisms, or an error in your assertions and/or proofs.
I'm still looking for a purpose for this video. A word of advice, and you're free to ignore it, of course: when making videos, state your purpose, why it's important, and then show it without making assumptions.
HarshColby 2 months ago
@HarshColby
I don't know why it's so hard for you to grasp the concept that scaffolding alone cannot account for the origin of IC molecular machines whose functions require multiple interacting components, and, this being the case, cooption is required. My purpose here is to show that scaffolding and EFR are not sufficient for generating such IC systems, and thus cooption is required. I will follow this video up with a critique of cooption.
Genomiques 2 months ago
@Genomiques I don't care (and nobody else does either) if scaffolding alone can't generate IC systems. I've already shown a case where cooption isn't required so I'll not bother to repeat it
Showing scaffolding and EFR alone are not sufficient is not the same as showing cooption is required.
imo, you should have started with your video on cooption and simply referred to the paper you quoted in these comments to make your point here. This video is pointless. It addresses a claim no one is making.
HarshColby 2 months ago
@HarshColby
"Showing scaffolding and EFR alone are not sufficient is not the same as showing cooption is required."
Other than invoking unknown evolutionary mechanisms, showing that actually does show that cooption is required.
By the way, it IS claimed by a number of critics of irreducible complexity that the Mullerian two-step does offer a solution to the problem of the origin of IC systems.
Genomiques 2 months ago
@Genomiques You have not shown that Mullerian two-step does not offer a solution. I haven't agreed that your argument in this video is valid. I simply didn't want to go around in circles and repeat what I've already said.
Yes, of course more than one protein is required for a great number of functions. This means it fits the definition of IC, but it says nothing about what combinations of mechanisms are involved in its evolution. What did you say that was different than what I said?
HarshColby 2 months ago
@HarshColby
You have conceded that many functions require multiple interacting proteins in order to exist. Thus, your general progression of how scaffolding would work, where you start with component A carrying out function X, a function which requires multiple interacting proteins, doesn't work because just one component cannot carry out function X.
Genomiques 2 months ago
@Genomiques Scaffolding can't work with an already IC component A to be part of a more complex IC system? Why not?
Perhaps you're talking about where the very first (simplest) IC system came from only? In that case, wouldn't such a simple system comprised of only two proteins be quite probable by randomness alone? At trillions of trials per second over the entire earth over millions of yrs, it seems inevitable. It's only the very complex systems that the IC argument would have any weight at all.
HarshColby 2 months ago
@HarshColby
No, no that' not what I'm saying. I'm saying that your scaffolding scenario starts with one component, A, and then B is added which later becomes necessary. But if A carries out a function that requires MULTIPLE interacting components, then how on earth is A alone supposed to carry out that function? In other words, your scaffolding scenario doesn't work, unless you invoke cooption.
Genomiques 2 months ago
@Genomiques Which is where we were days ago. For the sake of argument, okay, lets assume scaffolding requires cooption to create IC systems (whether or not A is IC btw so your "multiple interacting components" isn't really a factor in the new function). You cannot conclude from this, however, that scaffolding doesn't occur. You've simply established that for IC systems, new functionality may result. This isn't really about mechanisms, however. Yes, new functions are created, IC or not.
HarshColby 2 months ago
@HarshColby
I'm not and never did say that scaffolding doesn't occur. But since scaffolding alone cannot result in an IC molecular machine, then cooption is required. And if cooption is shown to have grave problems, then where does this leave us when it comes to explaining the origin of IC molecular machines?
Genomiques 2 months ago
@Genomiques But you haven't shown cooption does have problems, thus the topic of this video is pointless and/or incomplete. Make your video on cooption and state the conclusions of this video as a side note supported by the paper you quoted earlier. I can see how showing cooption is impossible would be important to evolutionary biology. Showing scaffolding may require cooption is a minor issue.
It sounds like you're using cooption as a synonym for a "change in function", and not the mechanism.
HarshColby 2 months ago
@HarshColby
I'm not going to show that cooption is impossible, because it clearly isn't. Gene duplication followed by sequence diversification leading to a shift in function has occurred. See, I'm not showing that scaffolding or cooption doesn't happen. I'm showing or going to show that those mechanisms aren't sufficient explanations for the origin of IC molecular machines.
Genomiques 2 months ago
@Genomiques Good luck with that. Many others have tried and failed. I will watch your cooption video and I'm sure we'll have an interesting conversation about it.
Word of advice: "molecular machines" is a subjective concept and only clouds the discussion. I'd suggest you stay away from that term if your intent is to present what you hope will be perceived as science.
HarshColby 2 months ago
@HarshColby
"Many others have tried and failed."
Indeed? I'd be interested in watching failed attempts to rebut the cooption scenario as an explanation for IC, here on YouTube - if that's what you meant.
Genomiques 2 months ago
@Genomiques Behe, for one, in Darwin's Black Box and in Edge of Evolution. Both of his extremely similar arguments fail miserably. In DBB, he argues cooption (and any other mechanism actually) can't help lead to IC systems, and in EE he argues it's highly improbable. Perhaps you have a novel approach.
HarshColby 2 months ago
@HarshColby
In EofE he mostly talks about the limits of evolution in terms of point mutations etc. If I recall correctly, he didn't spend too much time even discussing irreducible complexity (although he did discuss the IC state of the IFT system). Did he say *why* in both DBB and EofE cooption cannot lead to IC systems (or it's high improbability)?