[quote=“Bilbo, post:31, topic:784”]
If I understood Behe’s response, he would consider it a single binding site.[/quote]
But it isn’t a single site–it’s a pentameric channel. That means that one site on one monomer is interacting with a different site on another monomer. Two binding sites.
[quote]Since his edge is two binding sites, I don’t think it affects his calculations at all.
[/quote]What mathematical reasons would you have for saying that? Have you looked?
Hi @Joao,
To quote Behe: “Only one new binding site need develop for one area of a protein which binds to a different area of the same protein, to form a homogeneous complex with, say, C5 symmetry. That is all that is required for a circularly symmetric structure to form.” That was from here:
Behe’s two binding sites rule was that if more than two new binding sites are required in order to achieve some new function, then this would be beyond the edge. Not sure what else there is to look at. Meanwhile, you haven’t responded to his argument that the evolution of viral-cellular protein interaction is significantly different from, and much easier than, the evolution of cellular-cellular protein interaction.
[quote=“Bilbo, post:45, topic:784”]
To quote Behe: “Only one new binding site need develop for one area of a protein which binds to a different area of the same protein, to form a homogeneous complex with, say, C5 symmetry. That is all that is required for a circularly symmetric structure to form.”[/quote]
Quoting Behe doesn’t make him right. Moreover, you apparently didn’t read it well enough to catch the important qualifier “required.” The question neither you nor Behe are willing to address is not what is required, but whether that is what happened. Don’t we have the structure? Don’t we have the ancestral sequences? Stop playing hearsay games and engage with the evidence for yourself, Bilbo–if you dare.
It’s not a rule, it’s a hypothesis. Avoidance noted.
The math, Bilbo, for yourself. Engage your intellect. I asked you a straightforward question: what mathematical reasons would you have for saying that? Why won’t you answer?
[quote]Meanwhile, you haven’t responded to his argument that the evolution of viral-cellular protein interaction is significantly different from, and much easier than, the evolution of cellular-cellular protein interaction.
[/quote]Why should I? Behe’s false claim has nothing to do with viral-cellular protein interactions. Why are you trying to divert?
Have you considered starting with an open mind and going through the relevant data for yourself, instead of holding up someone who doesn’t bother to read the relevant primary literature as an authority?
Hi @Joao,
You’re welcome to correct Behe here, if you so desire. I’ll try to understand any math you wish to communicate. Otherwise, my point remains: Behe has responded to his major critics. And if his criterion is sound, then he seems to have provided a way of conducting a research program. I’m just curious why this wouldn’t be a “Lakatosian research program.”
[quote=“Bilbo, post:48, topic:784”]
You’re welcome to correct Behe here, if you so desire.[/quote]
I already did.
I’m asking what it does to the math that Behe already communicated. Do you not understand it? If so, why not just admit it?
Not substantively. Your refusal to engage mathematically constitutes implicit agreement–or at a minimum, no confidence in your claim.
[quote]And if his criterion is sound, then he seems to have provided a way of conducting a research program.[/quote]Then why isn’t anyone doing such research? And why do you call a hypothesis a “rule” or “criterion,” unless you want to avoid facing the fact that neither Behe nor anyone else has any intention of testing it?
Let’s see how well you understand the hypothesis: how many residues must be substituted to widen the substrate specificity of an enzyme to include an artificial substrate (significantly larger) without losing any ability to perform the original reaction it was “designed” to do? I hope that you understand that enzymes have to bind to their substrates.
I think you’re being too charitable here. I can easily show where important data are being ignored (see Bilbo above) and have zero problem mentally entering an ID “program.”
Example: the lens of the eye and its components were designed. This makes a clear empirical prediction: the major protein components of the lens that make it refractive, the crystallins, will have no statistically-significant similarities with other proteins with different functions.
There are three crystallins that can be used to test this hypothesis.
[quote=“system, post:1, topic:784”]
If one were to construct a program around it [ID], the core hypothesis would be “evolution via natural selection is insufficient to generate the diversity of life on this planet.” [/quote]
Why wouldn’t it be “life was intelligently designed”?
[quote]But this isn’t enough to build a research program,…
[/quote]I don’t see why not. There are obvious who, what, and when hypotheses that one can test empirically.
Hi @Joao
HIV evolving one new binding site does not challenge Behe’s math. I would suspect that a number of ID-friendly biologists already think they have discovered IC systems that they think were designed. But getting their conclusion printed in mainstream peer-reviewed journals probably won’t happen any time soon. I would consider that a philosophical bias on the part of the journals.
If I remember correctly, Behe argued that creating a new binding site typically required 5-6 amino acid changes. Whether or not that interferes with the original function of the protein probably depends upon where the changes take place. I believe it’s usually thought that changes take place in a duplicated gene, so that interference with the orignal protein doesn’t need to occur.
But Joao, let me ask you a question. What was the original post about?
[quote=“Bilbo, post:52, topic:784”]
HIV evolving one new binding site does not challenge Behe’s math.[/quote]
I asked how it changes it. Just speculate and apply the math, Bilbo. How would two change the math? I’m not asking you to agree, just apply the math.
Can you do it?
Why don’t they publish in Bio-Complexity then?
You have come to that conclusion on the basis of zero evidence! Is Behe doing anything empirical in his lab?
IIRC there was no argument, just a simple, empirical claim.
Hence my real-world question that you seem to be afraid to address: how many residues must be substituted to widen the substrate specificity of an enzyme to include an artificial substrate (significantly larger) without losing any ability to perform the original reaction it was “designed” to do?
Right in the substrate-binding site. What does Behe’s hypothesis predict?
No duplication in this case. Please apply Behe’s hypothesis and make a prediction.
[quote]But Joao, let me ask you a question. What was the original post about?
[/quote]Research programs. My point is that it’s easy to change perspectives–if one isn’t afraid of learning something. Are you?
Hi @Joao,
Perhaps you have misunderstood me. My contention here has been that if Behe’s argument is sound, then he has provided a sufficient condition for conducting a research program. I have not contended that I am able to fully defend Behe’s argument. I leave that debate to the reader.
In order to do research, money is needed. I suspect that there isn’t a whole lot of money available to do ID research to publish in any journal, ID friendly or not. But I’m basing my opinion that mainstream journals have a philosophical bias against ID research on the anecdotal experience of Behe: Correspondence with Science Journals | Discovery Institute
Meanwhile, if you wish to present a full-blown critique of Behe’s argument here, feel free to do so.
[quote=“Bilbo, post:54, topic:784”]
Perhaps you have misunderstood me. My contention here has been that if Behe’s argument is sound, then he has provided a sufficient condition for conducting a research program. [/quote]
Your explicit contention here was that two binding sites doesn’t change his math. I’m asking how you determined that mathematically.
But you did explicitly contend that two binding sites doesn’t change Behe’s math. Are you withdrawing that contention?
Yes, so what’s the budget of the DI? How much is Behe’s fellowship? Why would there be plenty of money for rhetoric, but none for research?
Then why did you speculate that the research has already been done? Why are you moving the goalposts from publication to funding?
I don’t see any bias against ID research, as Behe wasn’t trying to publish any research, just rhetoric. Do you not realize that Behe’s paper had ZERO research content? Do you not see the enormous gap between research and rhetoric?
Why not Bio-Complexity, then? Why do you specify “mainstream” when Behe’s on its editorial board?
[quote]Meanwhile, if you wish to present a full-blown critique of Behe’s argument here, feel free to do so.
[/quote]I think that I already have presented an empirical one, and you have implicitly accepted the validity of my critique by running away from the notion of applying his hypothesis to the real world.
Why is there any need to add to the full-blown critique in the first journal review Behe posted? The best part is this: “Meanwhile, metaphysicians should spare scientists their metaphysics and just let the scientists do their work–or join them in doing it.”
The lack of curiosity is fascinating. Why won’t Behe do any actual research to test his hypothesis?
I don’t recall saying that two binding sites would change Behe’s math. I do recall saying that one binding site doesn’t challenge his math. Behe has done peer-reviewed research to support his conclusions.
Saying it is 3 is just a start. It is what the mathematics indicate. A perfectly fair line of evidence.
We already know that freedom is real and relevant in the universe, so there is obviously going to be intelligent design occurring in the universe.
I don’t agree that a scientist doesn’t use common sense. If scientists are less knowledgable about how things are chosen in the universe than somebody not educated, but who is not prejudiced against it, then they have ceased to be scientists. The risk that scientists fail to notice the relevance of freedom in the universe is far greater than any mistake or inaccuracy that may occur in grounding intelligent design research.
[quote=“Bilbo, post:18, topic:2406, full:true”]
I don’t recall saying that two binding sites would change Behe’s math.[/quote]
Sorry, my error.
And I recall asking you how it changes his math, but for some reason you insist on a more violent verb.
I presume that you objected because two binding sites would make Behe’s math untenable. Would you mind explaining (mathematically, not with quotes from Behe) why one doesn’t change it, but two would apparently be catastophic? I can’t wrap my head around that mathematically.
[quote]Behe has done peer-reviewed research to support his conclusions.
http://www.lehigh.edu/~inbios/pdf/Behe/QRB_paper.pdf[/quote]
Bilbo, please! I’ve already explained to you why what Behe was unsuccessfully shopping around was not research, and now you hold up a review as “peer-reviewed research.” That’s simply not true. I’ve published 5 reviews. None were peer-reviewed. All were invited. I would never, ever hold them up as research productivity.
[quote]http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2286568/
[/quote]2004? Are you kidding? Behe has published nothing since then, and nothing empirical relevant to ID ever? He has a DI Fellowship (so he can do research) and he’s an editor of an ID journal (so he can easily publish research). What’s the problem in your opinion?
Isn’t that all the evidence we need to know that there’s nothing to see here? What do you think would happen to my NIH grant renewal application if I showed only one non-empirical paper even in three years and tried to pass off a review as research?
Prof Behe’s ignorance of population genetics is readily apparent to anyone who has done just the first set of readings on the topic. The arguments in Edge of Evolution fail on very basic grounds. I can elaborate if anyone is interested, but I think the critiques are easy enough to find online. Prof Venema has written about Behe and Edge, somewhat personally IIRC.
It is indeed odd that Bilbo cites the QRB review article as “peer-reviewed research,” but this might mean that Bilbo doesn’t understand how practising scientists use that phrase. The QRB article was probably peer reviewed, but it is a literature review on a focused topic and does not report original experimental data. If fact, it is clear that Prof Behe has never done experimental work on ID and has not participated in laboratory research since the late 1990s. (The 2004 publication involved simulation and made a claim that was promptly debunked.) More importantly, the QRB article is not relevant to any claim about multisite mutation or the evolution of multipart systems. I believe that remains the subject of our discussion?
Behe completely ignores fundamental population genetics. But the “irreducible complexity” challenge in his first book has stimulated thoughtful responses from practising scientists. See this paper by Lynch and Abegg and this very recent paper from Prof Joanna Masel’s group. Prof Masel has also written a delightful blog post on what evolutionary biologists can learn from creationists. Prof Behe has no standing in the professional evolutionary biology community, and could not without admitting that Edge of Evolution was a mistake. But a few biologists are willing to admit (perhaps grudgingly) that “irreducible complexity” is interesting. Count me among them.
[quote=“Humeandroid, post:21, topic:2406, full:true”]
Prof Behe’s ignorance of population genetics is readily apparent to anyone who has done just the first set of readings on the topic.[/quote]
I agree, but Bilbo doesn’t know that. I’m trying to get him to walk me through the math that he’s implicitly claiming to have evaluated.
Your statement is Eddieesque and not likely to be effective with Bilbo, as he can just frame it as your opinion vs. Behe’s.
Correct. Behe’s ignorance is staggering given that he is trying to rewrite fundamental population genetics to ignore existing variation so that he can pretend that there’s some sort of waiting required for mutations to happen.
[quote]But a few biologists are willing to admit (perhaps grudgingly) that “irreducible complexity” is interesting. Count me among them.
[/quote]Too bad Behe isn’t interested enough to do anything.
joao. a minimal ic system need at least 2-3 parts to its function. so if the chance to get a one part is about 10^10 then a 3 parts system need about 10^30 mutations. so to evolve a whale sonar for example we will need 10^30 mutations. its a lot.
You haven’t shown that whale sonar includes even a single new part, so your numbers, while large, are meaningless until you specify those parts.
Golly, didn’t I just point out an ID hypothesis about how The Designer designs and some empirical predictions that ID proponents should be testing for themselves?
IOW, dcscccc has clearly specified a style of design, with all or mostly new parts. While we don’t have a whale sonar parts catalog from The Designer, we have whole genomes (a whale parts catalog)!
If you’re so sure that there are completely new parts (you wouldn’t use such big numbers if you weren’t absolutely sure, right?) based on the way you are assuming how whales work, how many genes should be in the whale genome that aren’t in the human genome and vice versa?
ok joao. lets go on.
even if whale sonar evolve by a combination of parts from other systems, its not solve the problem but make it worse. because now we will need to explain how many systems evolve step wise. so its just push the problem to another system.
why i think that whale sonar have a unique parts? because we cant made a sonar by a combination of parts in a submarine. why do you think that the whale example is a different case?
[quote=“dcscccc, post:25, topic:2406, full:true”]
ok joao. lets go on.
even if whale sonar evolve by a combination of parts from other systems,…[/quote]
No, d, let’s start by not assuming evolution NOR design. Let’s start with something more simple: how whales work. Only then can we think clearly about evolution vs. design.
No, it doesn’t, because as you just showed, you understand neither evolutionary mechanisms nor developmental biology. Again, let’s test YOUR design hypothesis, not the one you are falsely attributing to evolution.
Thanks for being honest! But before we go further, why did you present something you merely think as something you know? And why are you not interested in understanding how the whale works before claiming that you know how it arose? What’s there to fear?
Exactly! You were never even considering evolution, much less hypothesizing it! You are really hypothesizing that the whale is designed, like a submarine. Your design hypothesis predicts that sonar will have newly-designed parts. Let’s test that prediction and see if your hypothesis holds up. Isn’t this fun?
[quote]why do you think that the whale example is a different case?
[/quote]Because I’ve studied molecular genetics and developmental biology.
Let’s question what you only think–but pretended to know–first. In science we question all of our assumptions. That teaches us a lot.
How many genes do you think are present in whales but not humans? I’ll give you one important piece of information: both whale and human have about 20,000 genes. How many should differ under YOUR hypothesis in which new parts are needed for new functions?
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