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Author | Topic: Recent paper with an ID spin? Abel and Trevors (2005). | |||||||||||||||||||
Smooth Operator Member (Idle past 5136 days) Posts: 630 Joined: |
quote:I already answered this. An I answered it where I was supposed to. Please leave this thread and don't bother me anymore.
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Smooth Operator Member (Idle past 5136 days) Posts: 630 Joined: |
quote:This is my last response to you. You are clueless about any kind of discussion that is going on. Your only argument is an ad hominem. You are constantly accusing me of religious bias. That is all you have to say. Therefore, goodbye and never talk to me again.
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Smooth Operator Member (Idle past 5136 days) Posts: 630 Joined: |
quote:Yes, it can be. Throw of a dice dictates a bug's life | New Scientist Bacteria can alter ther diet when 300 permease proteins are found within the cell, the cell swithches it's diet with geentic regulation. The cell than gains the ability to digest sugar. Now you claim it has been shown that CSI can increase with random mutations and natural selection. Please show me where.
quote:Why should I be proving a negative? You should give me evidence for your positive assertation. quote:That is simply how they do it. Measuring the conservation in different sequences is how they measure functionality. quote:That is true only after you ahve a protein. Before you have a protein all amino acides are equaly important, which is to say they are all not important in any way, since you have nothing to do with a bunch of ranom amino acids. quote:That's the same thing. One is based ony PFAM families the other is not. quote:Well, you need time to improve something. Why not just be still for some time and let them do their work? quote:That is the same thing. How can you measure conservation if you do not take into account whic amino acid has just changed from the previous sequence you measured? quote:I know it is, all of them are. I have not see any that is not based on Shannon's work. That is the basis for everything new in information theory. But Shannon's model alone is not enough. quote:I told you, it's a simple matter of extrapolation. There is nothing wrong here. You know very well that you can't just mutate proteins to infinity. quote:Yes it does. It's what Axe's work us used for. He did the work with proteins and changed them to where they stopped functioning as they should. This area of functionality, actualy the rpobability, is the number you need. quote:Again, Doug Axe. Please explain, what do you find wrong with his work? Why can't his work be extrapolated to find the modificational possibilities of RecA? quote:It's the best we got. Sure, you could make a better estimate, but not by much. I wouldn't be surprised if we even got a smaller number. You do know we can't get an infinity of possible modifications. Yet, that is what you are searching for. Or close to infinity. You simply won't get that. There is a limit. quote:Umm... yeah, I know. It's how extrapolation works. What's wrong with this experiment, except nothing? Do you think there are soem proteins that can be coded for with infinite numbers of sequences? quote:Very simple. You take a protein, you mutate it, and you find where the edge is. When the edge is passed, your protein becomes non-functional. All the working structures are still considered functional. All those functions could have been designed, or as you believe evolved from the start. So the more deformable the protein is, and retains it's function, the more chance we have for that protein to evolve. quote:Well if they could inflate the FSC, than what are we arguing about? They are not wrong. OK, I understand you have another objections. Please explain what else is wrong. quote:I do not care, simply because I do not use their way of measuring biological functions. And I also know evolution is supposed to build a flagellum, but has it ever been observed? Not really. Do we have anything from which we can extrapolate from? Not that I know of... quote:I'm not making anything up. Durston agrees that there is algorithmic information which is describing natural law. Simple chemical reactions are not biological functions. quote:It is nto enough, that is the point. You can also use random measure of information liek RSC and get a measure from some biological function. But that measure is wrong. Simply because it does not measure the functionality. quote:Because it is a natural law, like gravity. Ink will not fall on a piece of paper and produce a poem. Atoms of hydrogen and oxygen when they come together will form water. Amino acids will not form biological functions when they come together. There is no biological law to make them do that. quote:If that is true, than why does Durston, who des not agree with this, bases his work on Hazen's? quote:Ga ahead and extrapolate. I'm just asking you, from what are you going to extrapolate to what? quote:Of course it does. It measures specification, which can describe a function, and the amount of enteties like nucleotides, or aminoa cids, or proteins, needed to form that specification. That is the complexity and specification together, and it measures the information of biological functions.
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Smooth Operator Member (Idle past 5136 days) Posts: 630 Joined: |
quote:Hi WK. It doesn't matter that you posted a bit later. Since I also don't visit as often. Because I have more important things to do. As for Axe and Durston. I don't claim they're re right, because they say so, I just say what they wrote in their papers. That's all.
quote:Umm... I know that, that was my point alla long. It's like a light switch. It turns specific genes ON or OFF. So, tell me, how many times do you have to flip a light switch before you make the switch into something new? Never, obviously... Therefore, such changes are not evidence for evolution. quote:Actually, simple math says it can't be done. It's like saying that 2+2=5. We all know that is not true. You can't get anything more of than what you invested in the first place. A deterministic natural law, by definition can not add CSI into a system. Dembski in his book No Free Lunch, explains why in 2 ways. One is a more simpler, and another, a more complex mathematical proof. Here I will show you the simpler way. If you wan't to I can later on show you the more complex explanation. First we have a CSI j, and a detrministic natural law denoted by f. Natural laws are describet as functions. Simply because they act on a certain variable, and than give the same result every time. Just like 2X + 10 = 20. X will always be 5. In the same way, when you put water under 0C, you will always get ice. So now, you are claiming that this natural law "f", brought about CSI "j", without intelligent cause. That means that there was some element "i" in the domain of "f", that was acted upon by "f" and it brought upon "j". This is represented by the equation => "f(i) = j" This actually does not create new information, since "i" will always produce "j" when acted upon by "f". This simply means that the natural law has shifted the same amount of information from "i" to "j". The problem of where did the CSI come from is not resolved by this. Simply because we have to ask where did CSI in "i" come from? Because that is the same CSI as in "j". It just got shifted around by "f" acting upon it. Now we have this equation: "I(A&B) = I(A) + I(B|A)", let's call it "*". It explains that information in an event A and B equal information in the event A together with information B given that A is certain. Which basicly means that if A happens, B is sure to happen. Therefore, if we see that A happened, that means B happened too. Let us now use this equation in our example. Since we already know that "i" fully determines "j", with respect to "f", that means that "I(j|i) = 0". This means that if know all the information in "i", we will also know all the information in "j", when "f" acts upon "i". Which means that if "i" happens, "j" also happens, and whatever we learn from "i" we also learn from "j". And this means that we can learn nothing more from "j" than from "i". Meaning, information gained is equal to zero. Which means that CSI that was generated is not created by a natural law, it was simply shifted from some other place. All natural laws act like this. Therefore natural laws are precluded from creating CSI. They can only shift them around. If you want I cal also go through a more complex explanation in teh next post. No Free Lunch: Why Specified Complexity Cannot Be Purchased Without Intelligence - William A. Dembski - Google Knjige Read pages 151-152 for more... Oh, and you said CSI is not well defined. Please tell me why not?
quote:Their method is not supposed to tell us anything about all the possible functional sequences for that particular function. That is why they rely on Axe's work instead. quote:No, I'm not. I'm simply saying, that who cares about a bunch of amino acids. They are useless on their own. None of them is more important than the other. I mean, important to whome? quote:The only thing I can say I understood from you, is that you simply disagree with Durston's approach, simply because his method does not tell us about all the possible functions while measuring. And no, it's not supposed to. But than again, Axe's work comes into play here, and all gets sorted out. quote:I said "infinity" just to make a point. I know no sane person thinks you can mutate them to infinity. The point I was trying to make is that there is a limit. Which means not all sequences will work. quote:Well, if we extrapolate from what Axe has done, than I think we have no problem in determining the number of possible sequences. quote:If he mutated it beyond functionality than that is a good enough estimate. You can't get a totally right number down to one single sequence. quote:I have no problem with other data. If they show that proteins are even more deformable, and can still perform their function, than that's fine with me. Simply because my point remains. And that is, that there is a limit. And if we can estimate the limit, that there is nothing to stop us from measuring the functional information in the genome. quote:I know, I was simply trying to emphasize on the amount. Not to be taken literally. quote:If his estimate includes those sequences, than it can. Otherwise it can't. That's obvious. quote:No, that is just the conservation rate among all the proteins that are found. I can't see this inflating the FSC rate. quote:He is basing his work on Abel and Trevor's work, which I think you know about. The one where they talk about three subsets of sequence complexity. quote:You completely misunderstood me. I just wanted to say that RSC can measure anything, not that it is good enough to use as a measure of biological functions. Simply because it can not tell apart from biological functions, and simple natural sequences. It will always give you out some measure. quote:If I recal correctly. He is using a conservation rate. The same thing as you are using in other programs to measure functional sequence complexity. The only difference is that you think this one is, well, false... quote:I for one, would disagree on that simply because SELEX is actually not so random. The amount of intelligent input is to much to simply call it natural selection in action. As noted below. quote:NCBI quote:Long posts are just fine with me. The more we talk about, the more we can learn.
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Smooth Operator Member (Idle past 5136 days) Posts: 630 Joined: |
quote:What other supporting evidence? We have been through it all already. quote:Some do some don't. Some bases get marked so they can get removed or inputed in the sequence when the organims needs it. quote:In no way. But that is basicly my position. I am the one who is claiming new functions don't evolve, not you. quote:No, I do not have a problem, you have a problem. You are nitpicking. The reason I used that example is because it was easy to understand. I used it because of simplicity, to demonstrate determinism. To model a real natural law we would need millions of functions. I used just one to explain how determinism works. To model your example, we would just have to add another function. The result is the same in any case.
quote:Great, so we aggree, that natural forces do not create new information. They just transfer it to another place. quote:An object exhibits specified complexity when it conforms to an independently givven pattern and it's probabillity of occurance is bellow the UPB. I see nothing wrong with this definition.
quote:We are supposed to measure the sequences that can be aligned. Obviously we do not need to take into account distinct sequences. Their informational content is subsumed in the smaller ones. quote:No it's not. Like I said before. Amino acids by themselves, when they are not folded in a protein have no bearing on any biochemical investigation. If they did, than so do atoms in rocks. You do know that chemicals are made from atoms? So by your logic, we can find out something about life, if we study atoms all by themselves. No we can't. That's why amino acids by themselves are useless to biochemistry. Now chemistry is another story. It deals with chemicals by themselves... quote:If there are, well than, more power to them! I'm certainly not going to deny them that. Besides I never said Durston's method is the best. I was simply arguing from the start only that it existed. That is all. quote:To measure the conservation rate yes. There is nothing more I would add to it. quote:But you and I both know that he did not made it up. If you disagree with it than fine. But he did not just make it up. quote:To ephasize the point. Don't take it literally next time. quote:1.) He does not have to adress distinct structures, because they are in a field of their own. They should be calculated on their own. Not within this structure. The probability of a different structure is obviously different. 2.) Are you saying that he started mutating the gene from the middle or something? This is probablity we are working here with. We can't be sure that a result is correct to a single digit.
quote:Well no, obviously not. But he did more than that. He mutated the protein many times and concluded that it has some ability to adapt to mutations and still work. But not much. quote:I think that biological functions are what genes code for. That should be the most general definition. From what I can see I can find no flaw in Axe's work. quote:If we wanted to measure totally different structures than yes. But we are not trying to do that. As I said above, totally different structures, have totally different probabilities of arising. quote:No, since we are measuring the functional information for this specific function, and this specific protein sequence. Yes, with modifications. The protein can be modified. And from this point we measure the functional information. I understand your concern. And that is that there are other, totally different structures, that can do this same function. That's true, but we are not measuring them, now are we. We are trying to measure the probability of this structure, not the completely new one, which has different probability.
quote:Well we could under a general definition of biological information. And the only reson I defined it as an reduction in teh first place is because of a loss of specificity. quote:Well you see, that's the whole point. Natural selection has a constraint set on fitness. And therefore, it does not selct for new biological functions, but for fitness. Fitness and new biological functions are not correlated. That is why natural selection is as good as random search when it comes to building new biological structures. It has no teleology and it can not select those individuals that it needs to be something new. On the other hand, artificial selection, is teleological. It adds information by intelligently selecting the individuals that it wants.
quote:If you want to propose a better method than Axe's, than that is just fine with me. I have no problem with better methods in anything. I'm jsut saying that Axe's method is good also. Not that it is the best.
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