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Author Topic:   What is an ID proponent's basis of comparison? (edited)
Smooth Operator
Member (Idle past 5114 days)
Posts: 630
Joined: 07-24-2009


Message 286 of 315 (518499)
08-06-2009 10:52 AM
Reply to: Message 285 by Wounded King
08-06-2009 10:41 AM


quote:
Changed the structure.
And deteriorated it in the same time.
quote:
Changed the information, without affecting the function. Aren't you the one making posts supporting the idea of function as an essential component of measuring information in sequence analyses? If so how are you measuring the information change/loss in this case where you admit it doesn't affect the function?
It is possible to change the structure without affecting the function. But not in the long run.
quote:
Change of structure = change of form? = change of information?
Exactly, what's the problem?
quote:
Except if you knew any biology you would know that a change in the primary sequence of a protein doesn't necessarily mean a change in the higher level structures. So in fact in many cases a change in the primary structure will not lead to any change in the secondary or tertiary. There are obvious instances where this is not the case, as with the sickle cell anaemia example, but a change in primary sequence need not lead to a change in the higher levels of structure, as you would know if you understood biology. The fact that enough changes will cause a change doesn't mean that any specific change necessarily does, for example not every mutation in haemoglobin leads to sickle cell.
Neither did I say it does. I sad that OVER LONG PERIODS OF TIME, these kind of changes lead to loss of functions.
quote:
This doesn't get any truer just because you keep repeating it. Other than through its effect on function how can you justify characterising this as a deterioration? Can you quantify the informational loss in the absence of a change in function? If so how?
If it was caused by a random change and if the structure is not in it's original form that it is a deterioration.
quote:
You simply assume that any change in the amino acid sequence is a loss of information, but there is no reason for anyone else to drink your cool aid unless you can make a more compelling argument than simply repeating your contention ad nauseam.
I'm claiming this becasue natural forces do not build up but deteriorate the genome. So there is noreson to believe that slight changes do add information.

This message is a reply to:
 Message 285 by Wounded King, posted 08-06-2009 10:41 AM Wounded King has replied

Replies to this message:
 Message 290 by Wounded King, posted 08-07-2009 3:12 AM Smooth Operator has replied

Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.3


Message 287 of 315 (518529)
08-06-2009 1:03 PM
Reply to: Message 284 by Smooth Operator
08-06-2009 10:22 AM


Smooth Operator writes:
There is no information in the rocks in the first place. The information that there are three rocks comes from me.
Again, recall that with eyes closed you could not know the number of rocks. You had to look at the rocks in order to know how many there were. The information about the number of rocks did not originate with you. You did not create the information about the number of rocks. You merely translated the information about the number of rocks that was encoded into the light reaching your eyes into information on a piece of paper.
Here's another way of looking at it. Let's say you ask me to go into the woods and count for you the number of rocks in the first clearing I come to. I do this and find a clearing with three large rocks. I decide to communicate this information to you by going to your house and dragging three large rocks into your front yard. You then look at these three rocks and know that there were three rocks in the clearing. If your view about information were correct then when you look at three rocks that a person dragged in, that it would be information communicated to you, but when you look at three rocks that natural forces just happened to leave there then that would be information you created yourself. That's contradictory and makes no sense. Three rocks are three rocks, no matter who or what put them there and no matter whether there was any conscious intent involved.
quote:
There is no law that states that information can only come from a mind.
It's not a law, it's something that has never been observed. Therefore I should not believe it.
You think that information includes meaning and I don't. If we're talking about Shannon information then you're wrong. If we're talking about Gitt information then I'm wrong. But Shannon information is the only definition that has any scientific legitimacy. If you think otherwise then just provide references to Gitt's research papers. I can save you the time, though. If you go to Google Schoolar and look up Werner Gitt you'll find these papers (I only include the ones in English) appear first:
  • In the Beginning Was Information (Christliche Literatur-Verbreitung)
  • What About The Other Religions? (Christliche Literatur-Verbreitung)
  • Wonder of man (Christliche Literatur-Verbreitung)
  • Information, science and biology (Creation Ministries International)
  • Stars and Their Purpose: Signposts in Space (Christliche Literatur-Verbreitung)
  • Dazzling desing in miniature (Creation ex nihilo)
  • Did God use Evolution? (Christliche Literatur-Verbreitung)
"Christliche Literatur-Verbreitung" means "Christian Literature Distribution". So only Christian organizations publish Werner Gitt's papers. There's been no scientific peer review, no publication in scientific journals, no acceptance within the scientific community. And in fact, if you look at the Abel/Trevors, the Durston, and the Capra papers, you'll find that Gitt isn't referenced. Scientifically he's a non-entity.
Now I went through all this only to show that Gitt's views are not currently accepted within the scientific community. It isn't that he's wrong, but that he hasn't yet been found right. You shouldn't be citing Gitt as if his views had any legitimacy, because that is not the case. You shouldn't be reciting Gitt's list from statistics to apobetics and saying, "That's what information is," because it's only what Gitt says information is. No one in science agrees, and since he's never published in any scientific journals, Gitt isn't even offering his ideas to the scientific community for consideration.
What we have that is quantifiable is Shannon information.
Out performs random search in what? Selecting the fitest? Could be.
Well, let's be less equivocal about this. As far as selecting the fittest, natural selection is orders of magnitude superior to random selection.
But not in getting you new biological functions.
Evolution doesn't proceed in jumps of new biological functions. The bacteria in each new generation experience mutations that make them only very, very slightly different from the previous generation. It is these very slight differences that are being acted upon by natural selection. Completely new biological functions arising in a single generation are extremely unlikely to occur and be submitted to the selection mechanism, whether it be random selection or natural selection.
This is not a biological function! What are you talking about? Do you even know how sickle cell works? It DEFORMS red blood cells so malaria can't attach to them very well. This is not a biological function, this is deterioration of red blood cells.
Blood has a biological function (a number of them, actually), and sickle cell anemia affects its function. It worsens its ability to distribute nutrients to the body, and it improves its ability to provide resistance to maleria.
That is because nature does not select fitness in correlation to biological functions.
This could only be true if fitness were not a function of the biological functioning of organisms. But the two are intimately related. It could be no other way. A change in a gene causes a change in the protein it builds which causes a change in in the way the teeth form which is a change in biologic function. This change in the biology function forming the teeth causes a change in their sharpness which has an effect on fitness.
Biological functions are expressed outwardly by the organism, and this outward expression affects fitness.
--Percy

This message is a reply to:
 Message 284 by Smooth Operator, posted 08-06-2009 10:22 AM Smooth Operator has replied

Replies to this message:
 Message 288 by Smooth Operator, posted 08-06-2009 1:33 PM Percy has replied

Smooth Operator
Member (Idle past 5114 days)
Posts: 630
Joined: 07-24-2009


Message 288 of 315 (518538)
08-06-2009 1:33 PM
Reply to: Message 287 by Percy
08-06-2009 1:03 PM


quote:
Again, recall that with eyes closed you could not know the number of rocks. You had to look at the rocks in order to know how many there were. The information about the number of rocks did not originate with you. You did not create the information about the number of rocks. You merely translated the information about the number of rocks that was encoded into the light reaching your eyes into information on a piece of paper.
There is no information about the number of rocks outside of me. The rocks themselves represent rocks, not the information about their number.
quote:
Here's another way of looking at it. Let's say you ask me to go into the woods and count for you the number of rocks in the first clearing I come to. I do this and find a clearing with three large rocks. I decide to communicate this information to you by going to your house and dragging three large rocks into your front yard. You then look at these three rocks and know that there were three rocks in the clearing. If your view about information were correct then when you look at three rocks that a person dragged in, that it would be information communicated to you, but when you look at three rocks that natural forces just happened to leave there then that would be information you created yourself. That's contradictory and makes no sense. Three rocks are three rocks, no matter who or what put them there and no matter whether there was any conscious intent involved.
That's not contradictory becasue the three rocks in teh first place are not trying to inform me of anything. They are simply there. If I asked somebody to bring me some rocks, and he does so, than I know that this was done by an intelligent agent, and thus is information created by this agent. Than when I see the rocks, I simply read the information somebody created.
quote:
You think that information includes meaning and I don't.
Well you are simply wrong. It does. This has nothing to do what you think. It's not up to debate. It's a well known fact.
quote:
Information as a concept has a diversity of meanings, from everyday usage to technical settings. Generally speaking, the concept of information is closely related to notions of constraint, communication, control, data, form, instruction, knowledge, meaning, mental stimulus, pattern, perception, and representation.
Information - Wikipedia
Tell me, how can you have knowledge without meaning? You can't it's insane to even think you can.
quote:
If we're talking about Shannon information then you're wrong.
But I'm not talking about Shannon Information. Shannon Information is not information in general. It's only a MODEL of information suitable in engineering.
quote:
But Shannon information is the only definition that has any scientific legitimacy.
Is this a fact or an opinion?
quote:
"Christliche Literatur-Verbreitung" means "Christian Literature Distribution". So only Christian organizations publish Werner Gitt's papers. There's been no scientific peer review, no publication in scientific journals, no acceptance within the scientific community. And in fact, if you look at the Abel/Trevors, the Durston, and the Capra papers, you'll find that Gitt isn't referenced. Scientifically he's a non-entity.
I don't care. Really I don't care. If you can't refute his claims an you have to resort to PR than you already lost this discussion.
quote:
Now I went through all this only to show that Gitt's views are not currently accepted within the scientific community. It isn't that he's wrong, but that he hasn't yet been found right. You shouldn't be citing Gitt as if his views had any legitimacy, because that is not the case. You shouldn't be reciting Gitt's list from statistics to apobetics and saying, "That's what information is," because it's only what Gitt says information is. No one in science agrees, and since he's never published in any scientific journals, Gitt isn't even offering his ideas to the scientific community for consideration.
No, he is right. Just becasue you do not accept it, doesn't mean anything. And no, I didn't say that he is the only one who says it, other people do to. It's a well known fact. It's only you who doesn't understand the difference between Shannon information and information in general. If you think he is wrong, fine, but explain why.
quote:
What we have that is quantifiable is Shannon information.
I know we do. And Gitt's theories aren't even supposed to be quantifiable. Not yet that is. I said so myself. He was talking what information is in general. Do you understand the difference?
quote:
Well, let's be less equivocal about this. As far as selecting the fittest, natural selection is orders of magnitude superior to random selection.
Not really, if you read Genetic entropy you would know better. But never mind. Let's say that it is as you say. Still, selection for the fittest does not get you selection for the new biological functions.
quote:
Evolution doesn't proceed in jumps of new biological functions. The bacteria in each new generation experience mutations that make them only very, very slightly different from the previous generation. It is these very slight differences that are being acted upon by natural selection. Completely new biological functions arising in a single generation are extremely unlikely to occur and be submitted to the selection mechanism, whether it be random selection or natural selection.
But they are never going to arise becasue natural selection is as good as blind chance in selecting for new biological functions. Yes, even if we agree that it's better at selecting for fitness than blind chance.
quote:
Blood has a biological function (a number of them, actually), and sickle cell anemia affects its function. It worsens its ability to distribute nutrients to the body, and it improves its ability to provide resistance to maleria.
But resistance to malaria is a byproduct, not a biological function like the ATP syntahse performs. It's just the INABILITY of malaria to attach it'self to red blood cells, not a new ABILITY.
quote:
This could only be true if fitness were not a function of the biological functioning of organisms. But the two are intimately related. It could be no other way. A change in a gene causes a change in the protein it builds which causes a change in in the way the teeth form which is a change in biologic function. This change in the biology function forming the teeth causes a change in their sharpness which has an effect on fitness.
Biological functions are expressed outwardly by the organism, and this outward expression affects fitness.
You are totally missing the point. YOu simply dont' get it. Why? What is so hard to understand here?
Just becasue natural selection has a target for fitness, doesn't mean that this target is the same as NEW, and again, I repaet, NEW, not old, but NEW, do you get it now, NEW, NEW, NEW biological function that does not exist yet.
Evolution would ahve to evolve some new function by selecting few nucleotides at a time, one generation at a time. But natural selection has no information about this specific function, and it doesn't know that it is supposed to search for it. It doesn't know what sequence it needs to get this new function.
Yes, it will select for those who are more fit, but the sequence for fitness does not correlate for a biological function that does not already exist. Which part of this do you not understand?
Natural selection is not looking for sequences that have new biological function, it's looking for the fittest. Those two are not correlated. Yes, effective biological functions and fitness in most cases are, but NEW biological functions are not.
So natural selection works better than a blind search for fitness, but not for something that it's not even looking for, and that is NEW biological functions.
Because it's not looking for them, so it doesn't know if it should keep a nucleotide or not. It can't think in advance. It can't keep a nucleotide and build up a sequence that will be a new biological function because it is not trying to do so. It's only trying to keep the most fit, REGARDLESS if thier genomes are gaining new biological functions.
That's why in searching for sequences that perform new biological functions, natural selection equals blind search.

This message is a reply to:
 Message 287 by Percy, posted 08-06-2009 1:03 PM Percy has replied

Replies to this message:
 Message 289 by Percy, posted 08-06-2009 8:06 PM Smooth Operator has replied

Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.3


Message 289 of 315 (518615)
08-06-2009 8:06 PM
Reply to: Message 288 by Smooth Operator
08-06-2009 1:33 PM


Smooth Operator writes:
There is no information about the number of rocks outside of me.
That you keep saying this makes no sense. If the only information about the number of rocks were inside you then you would know it with your eyes closed. But you don't. You have to open your eyes and look at the rocks before you know how many there are. Without information flowing to you from your environment it isn't possible for you to know anything about it.
That's not contradictory becasue the three rocks in teh first place are not trying to inform me of anything. They are simply there. If I asked somebody to bring me some rocks, and he does so, than I know that this was done by an intelligent agent, and thus is information created by this agent. Than when I see the rocks, I simply read the information somebody created.
I already know you think that information can only be created by an intelligence. In response to examples illustrating that this is not so you're just repeating this baseless assertion over and over again.
Let me try again, and hopefully this time you'll respond with an explanation rather than another unsupported declaration.
If I record the number of rocks in the clearing on a piece of paper and hand it to you, then you can read that piece of paper and now information is being communicated from the paper to you. If I instead record the information by dragging three rocks into your yard to indicate the number, these rocks communicate information to you about the number of rocks in the clearing.
But what if the rocks were in *my* yard and you don't know how they got there. You'll see the three rocks and know that therefore there were three rocks in the clearing, and it doesn't matter whether I put them there or they were always there.
quote:
You think that information includes meaning and I don't.
Well you are simply wrong. It does. This has nothing to do what you think. It's not up to debate. It's a well known fact.
You're again breaking up longer explanations into little unrelated pixels and thereby failing to grasp what is being said. That statement you just replied to was part of a longer explanation about how we're actually using two different definitions of information. I say you're wrong about meaning being part of information, and I'm talking about Shannon information. You say I'm wrong to exclude meaning from information, and you're talking about Gitt information.
The real issue is whether there's any validity to Gitt information, and I explained that there is not. Your response basically comes down to, "Is too!"
But I'm not talking about Shannon Information. Shannon Information is not information in general. It's only a MODEL of information suitable in engineering.
You keep issuing this bald statement but never supporting it. If information theory can't be applied to DNA (and a broad range of other areas, including physics and chemistry) then explain how this is wrong (you might recognize this example, I keep repeating it along with requests for you to address it beyond saying, "No, you're wrong."):
Consider a specific gene in a population of bacteria that has three alleles we'll call A, B and C. For lurkers not familiar with the term, alleles are variants of a single gene. One familiar example is eye color. The eye color gene has several alleles: brown, blue, green, etc. Human eye color depends upon which one you happen to inherit. Eye color isn't really this simple of course, but this hopefully gets the idea of alleles across.
So every bacteria in the population has either the A allele, the B allele or the C allele. We can calculate how much information is required to represent three alleles in this bacterial population. It's very simple:
log23 = 1.585 bits
Now a random mutation occurs in this gene during replication and the D allele appears. Through the following generations it gradually spreads throughout the population and becomes relatively common. There are now four alleles for this gene, A, B, C and D. The amount of information necessary to represent four alleles is:
log24 = 2 bits
The amount of information required to represent this gene in the bacterial population has gone from 1.585 to 2 bits, an increase of .415 bits, and an example of random chance increasing information.
Moving on:
quote:
Information as a concept has a diversity of meanings, from everyday usage to technical settings. Generally speaking, the concept of information is closely related to notions of constraint, communication, control, data, form, instruction, knowledge, meaning, mental stimulus, pattern, perception, and representation.
Information - Wikipedia
You're your own worst enemy. This is a general definition of information, and it attempts to cover its meaning in a number of different contexts. One of the meanings it covers is Shannon information. Gitt information and apobetics and all that is nowhere to be found in that article. Gee, now why would that be?
quote:
But Shannon information is the only definition that has any scientific legitimacy.
Is this a fact or an opinion?
Keeping in mind that I was contrasting Shannon and Gitt information, of the two, Shannon information is the only one with any scientific legitimacy. Yes, that's a fact. As I said before, Gitt has never even submitted his ideas to scientific journals. All his work is published by Christian and creationist organizations.
I don't care. Really I don't care. If you can't refute his claims an you have to resort to PR than you already lost this discussion.
I *have* refuted Gitt's positions. You're response to the refutations has in effect been, "No, you're wrong."
I know we do. And Gitt's theories aren't even supposed to be quantifiable. Not yet that is. I said so myself. He was talking what information is in general. Do you understand the difference?
First, no, we're not talking about general definitions of information. We're talking about Gitt information versus Shannon information. Here's another refutation to Gitt information: Gitt information states that the information in DNA that codes for proteins has meaning. He further states that only an intelligence can create new information because only an intelligence can create meaning. However, he can't quantify meaning, so he cannot compare the amount of meaning before and after a mutation, and so has no way to know whether the meaning has increased or decreased. Therefore he can't demonstrate that only an intelligence can create information.
quote:
Well, let's be less equivocal about this. As far as selecting the fittest, natural selection is orders of magnitude superior to random selection.
Not really...
Yes, really. Evolution is far superior to random. Here's why.
Let's say our population of bacteria numbers 109, and that its DNA has 106 base pairs. With a mutation rate of 10-8 per base pair per generation, one out of a hundred bacteria will experience a mutation each generation, which means that if the population remains level that 107 bacteria in each generation will have a single mutation (this is only approximate, I'm not going to go through the actual precise math).
If we assume that it only takes a single point mutation to evolve the ability to metabolize the alternative and abundant nutrient, then once in every hundred generations one of the bacteria will experience the necessary mutation. If the time it takes for a generation is 20 minutes, then the necessary mutation will appear every 33 hours.
In order for the population to remain constant, half the bacteria in each generation must die. In your random algorithm the bacterium with the necessary mutation has only a 50% chance of being selected. If it survives then in the next generation the two bacteria have a 25% chance of both not making it to the next generation. The math gets more complicated after that because of the number of permutations.
In the evolution algorithm with the mutated bacterium's advantage of being able to metabolize the abundant nutrient it has a nearly 100% chance of being selected.
You are totally missing the point. YOu simply dont' get it. Why? What is so hard to understand here?
Gee, you don't sound bored anymore!
Have you ever considered the possibility that you're the one who's not getting it? Just a thought.
Just becasue natural selection has a target for fitness, doesn't mean that this target is the same as NEW, and again, I repaet, NEW, not old, but NEW, do you get it now, NEW, NEW, NEW biological function that does not exist yet.
Gee, I directly addressed this in the message you're replying to. Quoting myself in Message 284, I said:
Percy in Message 284 writes:
Evolution doesn't proceed in jumps of new biological functions. The bacteria in each new generation experience mutations that make them only very, very slightly different from the previous generation. It is these very slight differences that are being acted upon by natural selection. Completely new biological functions arising in a single generation are extremely unlikely to occur and be submitted to the selection mechanism, whether it be random selection or natural selection.
In other words, there's no such thing as new biological functions. There's only functions that are very slightly changed.
Because it's [natural selection] not looking for them [new biological functions], so it doesn't know if it should keep a nucleotide or not. It can't think in advance. It can't keep a nucleotide and build up a sequence that will be a new biological function because it is not trying to do so. It's only trying to keep the most fit, REGARDLESS if thier genomes are gaining new biological functions.
Yes, this is correct. Evolution is undirected. It selects what is best for survival in the current generation under the current environmental conditions. Evolution has no idea where it is going, it has no goal beyond survival in the present, but it has to end up somewhere. Each possible somewhere is incredibly unlikely, but no particular somewhere was preselected. The odds of arriving at one of the possible somewheres is 100%.
Here's another way to look at the odds. Given all the possibilities and options and choices in your life, what are the chances that you'd be where you are right now reading this message? Pretty tiny, right? But you have to be somewhere, and this is where you ended up, no matter how unlikely it might be. The odds of you ending up at one of the possible outcomes in your life is again 100%.
--Percy

This message is a reply to:
 Message 288 by Smooth Operator, posted 08-06-2009 1:33 PM Smooth Operator has replied

Replies to this message:
 Message 291 by Smooth Operator, posted 08-08-2009 4:49 PM Percy has replied

Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 290 of 315 (518646)
08-07-2009 3:12 AM
Reply to: Message 286 by Smooth Operator
08-06-2009 10:52 AM


Exactly, what's the problem?
That a change in information need not be a net loss of information as you assume.
Neither did I say it does. I sad that OVER LONG PERIODS OF TIME, these kind of changes lead to loss of functions.
Which is totally irrelevant to this specific case. If a mutation causes no change in function then please tell me how you measure the change in information involved and determine it to be a net loss?
If it was caused by a random change and if the structure is not in it's original form that it is a deterioration.
Only if you assume the 'original' structure, which is in fact just the structure as we first assayed it or what we have determined to be ancestral, is some sort of functional ideal. But if a change causes no net loss of information or function how can you characterise it as deterioration.
TTFN,
WK

This message is a reply to:
 Message 286 by Smooth Operator, posted 08-06-2009 10:52 AM Smooth Operator has replied

Replies to this message:
 Message 292 by Smooth Operator, posted 08-08-2009 4:49 PM Wounded King has replied

Smooth Operator
Member (Idle past 5114 days)
Posts: 630
Joined: 07-24-2009


Message 291 of 315 (518824)
08-08-2009 4:49 PM
Reply to: Message 289 by Percy
08-06-2009 8:06 PM


quote:
That you keep saying this makes no sense. If the only information about the number of rocks were inside you then you would know it with your eyes closed. But you don't. You have to open your eyes and look at the rocks before you know how many there are. Without information flowing to you from your environment it isn't possible for you to know anything about it.
That's true, but the rocks do not represent information, they represent themselves.
quote:
I already know you think that information can only be created by an intelligence. In response to examples illustrating that this is not so you're just repeating this baseless assertion over and over again.
The point remains that you do not understand what information is. Bunch of rocks in not information. Bunch of rocks in not knowledge. If you want to use those rocks to create some knowledge about them than fine. But the rocks did not create knowledge about them. They are simply there.
quote:
Let me try again, and hopefully this time you'll respond with an explanation rather than another unsupported declaration.
If I record the number of rocks in the clearing on a piece of paper and hand it to you, then you can read that piece of paper and now information is being communicated from the paper to you. If I instead record the information by dragging three rocks into your yard to indicate the number, these rocks communicate information to you about the number of rocks in the clearing.
But what if the rocks were in *my* yard and you don't know how they got there. You'll see the three rocks and know that therefore there were three rocks in the clearing, and it doesn't matter whether I put them there or they were always there.
But than the last case is no information at all. We did not agree on any syntax. We did not agree that you are going to give me information about the rocks, therefore they do not represent anything.
quote:
You're again breaking up longer explanations into little unrelated pixels and thereby failing to grasp what is being said. That statement you just replied to was part of a longer explanation about how we're actually using two different definitions of information. I say you're wrong about meaning being part of information, and I'm talking about Shannon information. You say I'm wrong to exclude meaning from information, and you're talking about Gitt information.
There is no such thing as "Gitt Information". He just explained what information is in general.
quote:
The real issue is whether there's any validity to Gitt information, and I explained that there is not. Your response basically comes down to, "Is too!"
You didn't explain anything. You just said that he was a nobody in scientific community. Is that an explanation?
quote:
You keep issuing this bald statement but never supporting it. If information theory can't be applied to DNA (and a broad range of other areas, including physics and chemistry) then explain how this is wrong (you might recognize this example, I keep repeating it along with requests for you to address it beyond saying, "No, you're wrong."):
I never said that. Information theory can be applied to biology. It's just the particular model from that theory that it can't. And that's Shannon model.
And why do you keep quoting that part about the alleles? Pure number of genes tell you nothing about how many biological functions they code for.
quote:
You're your own worst enemy. This is a general definition of information, and it attempts to cover its meaning in a number of different contexts. One of the meanings it covers is Shannon information. Gitt information and apobetics and all that is nowhere to be found in that article. Gee, now why would that be?
I knwo it's in general for God's sake! I have been telling you that for the last 20 pages.
And yes, it covers a lot of aspects of information, including Shannon, knowledge, and meaning. And those last two you said had nothing to do with information. You were clearly wrong. It also doesn't have to mention Gitt. He is not well known as Shannon.
quote:
Keeping in mind that I was contrasting Shannon and Gitt information, of the two, Shannon information is the only one with any scientific legitimacy. Yes, that's a fact. As I said before, Gitt has never even submitted his ideas to scientific journals. All his work is published by Christian and creationist organizations.
Again, there is not such thing as "Gitt Information".
quote:
I *have* refuted Gitt's positions. You're response to the refutations has in effect been, "No, you're wrong."
Saying that he is nobody and doesn't publish in PR articles is not a refutation.
quote:
First, no, we're not talking about general definitions of information.
Well I am talking about what information is in general when I'm talking about Gitt.
quote:
We're talking about Gitt information versus Shannon information.
For teh third time. There is not such thing as "Gitt Information".
quote:
Here's another refutation to Gitt information: Gitt information states that the information in DNA that codes for proteins has meaning. He further states that only an intelligence can create new information because only an intelligence can create meaning. However, he can't quantify meaning, so he cannot compare the amount of meaning before and after a mutation, and so has no way to know whether the meaning has increased or decreased. Therefore he can't demonstrate that only an intelligence can create information.
He doesn't have to, he is talking in general. To quantify the first three levels of information we can use Dembski's model of CSI. Using this model we can clearly see that mutations do not generate CSI.
quote:
Yes, really. Evolution is far superior to random. Here's why.
Let's say our population of bacteria numbers 109, and that its DNA has 106 base pairs. With a mutation rate of 10-8 per base pair per generation, one out of a hundred bacteria will experience a mutation each generation, which means that if the population remains level that 107 bacteria in each generation will have a single mutation (this is only approximate, I'm not going to go through the actual precise math).
If we assume that it only takes a single point mutation to evolve the ability to metabolize the alternative and abundant nutrient, then once in every hundred generations one of the bacteria will experience the necessary mutation. If the time it takes for a generation is 20 minutes, then the necessary mutation will appear every 33 hours.
In order for the population to remain constant, half the bacteria in each generation must die. In your random algorithm the bacterium with the necessary mutation has only a 50% chance of being selected. If it survives then in the next generation the two bacteria have a 25% chance of both not making it to the next generation. The math gets more complicated after that because of the number of permutations.
In the evolution algorithm with the mutated bacterium's advantage of being able to metabolize the abundant nutrient it has a nearly 100% chance of being selected.
Well you are obviously wrong. This is only a theoretical model that does not work that good. The problem is in the noise. There is to much of those who are not as fit as others, so on average the have more chance than the fit ones to reproduce. Therefore effectively shutting down natural selection for beneficial mutations. Some may pass if the pressure is really hard, but not if it is relaxed.
Just a moment...
The Crow paper talks about human fitness deteriorating 1-2% in one generation. If natural selection was so great than we would not have this problem. Crow collected data on mutation rates an accumulation of them in the genome. He came to the conclusion that the human genome is deteriorating.
The other problem are near neutral mutations (NNM). They are deleterious, and by definition so weak that natural selection does not select against them. Therefore they keep accumulating in the genome. Over time they cause genetic meltdown and the species dies.
NCBI
This is discussed in the Kimura paper. See the graph? Notice the darker part of the graph. It's the NNMs. They keep accumulating in the genome.
quote:
In other words, there's no such thing as new biological functions. There's only functions that are very slightly changed.
And those slight changes do not lead over time to totally new functions. If evolution was true single celled organisms evolved to people. Over vast amounts of time they gained a lot of information. They gained new functions. The only problem is those slight changes are accumulating, but not in a way to get you such a change that you see between a single celled organims and a human.
quote:
Yes, this is correct. Evolution is undirected. It selects what is best for survival in the current generation under the current environmental conditions. Evolution has no idea where it is going, it has no goal beyond survival in the present, but it has to end up somewhere. Each possible somewhere is incredibly unlikely, but no particular somewhere was preselected. The odds of arriving at one of the possible somewheres is 100%.
Here's another way to look at the odds. Given all the possibilities and options and choices in your life, what are the chances that you'd be where you are right now reading this message? Pretty tiny, right? But you have to be somewhere, and this is where you ended up, no matter how unlikely it might be. The odds of you ending up at one of the possible outcomes in your life is again 100%.
And this is where you are painfully wrong again. Evoluton has got to get you new biological functions if you are going to evolve from a bacteria to a man. Yes, the odds that something is going to happen is 1:1. But in this case, you are not looking for anything. You are looking for something. Even though evolution isn't. That's why I said fitness and new functions are not correlated.
There is only so much of biological functions you can have. Some sequences of nucleotides do not code for any meaningful biological functions. That is, a vast majority does not, from the vast amount of all possible sequences. Only a tiny minority does. So you see, you need to get to those relevant biologically meaningful sequences, with an evolutionary algorithm that does not search for them!
The 3 billion base pairs of human genome go something like this:
"GATCGACGACGATTATGCATCTAGCCGCGATTACTAGCTACG..."
This is biologically relevat sequence. Let's say it codes for an eye. Just an example.
Now imagine that you had this kind of genome:
"TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT..."
You do understand that 3 billion Ts is not going to code for anything. It has absolutly no biological function. If the whole genome was just 3 billion Ts, there would be no people. Because in the genetic code nothing is represented with just Ts. It's the same thing if you wrote 30 Ts in English language. It's meningles, it represents nothing.
So again, the conclusion is, that evolution is as good from searching the new biological functions as random chance.

This message is a reply to:
 Message 289 by Percy, posted 08-06-2009 8:06 PM Percy has replied

Replies to this message:
 Message 293 by Percy, posted 08-09-2009 9:52 AM Smooth Operator has replied

Smooth Operator
Member (Idle past 5114 days)
Posts: 630
Joined: 07-24-2009


Message 292 of 315 (518825)
08-08-2009 4:49 PM
Reply to: Message 290 by Wounded King
08-07-2009 3:12 AM


quote:
That a change in information need not be a net loss of information as you assume.
I never said that. I said it can be fine tuning.
quote:
Which is totally irrelevant to this specific case. If a mutation causes no change in function then please tell me how you measure the change in information involved and determine it to be a net loss?
They do in vast majority of cases. Even if they don't. Even if they just damage the structure slightly, next few mutations will damage it enough to destroy the function.
quote:
Only if you assume the 'original' structure, which is in fact just the structure as we first assayed it or what we have determined to be ancestral, is some sort of functional ideal. But if a change causes no net loss of information or function how can you characterise it as deterioration.
No, it doesn't have to be an ideal. A new house is an ideal. If you throw a rock at it and damage it, it lost some of it structure. It's not an ideal anymore. But a further rock throw, and damage to the house is still more of a net loss.

This message is a reply to:
 Message 290 by Wounded King, posted 08-07-2009 3:12 AM Wounded King has replied

Replies to this message:
 Message 294 by Wounded King, posted 08-09-2009 6:50 PM Smooth Operator has replied

Percy
Member
Posts: 22392
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.3


Message 293 of 315 (518894)
08-09-2009 9:52 AM
Reply to: Message 291 by Smooth Operator
08-08-2009 4:49 PM


Hi Smooth Operator,
I'm a little reluctant to reply because we've gotten to the point where I'm having trouble avoiding explaining to you what an explanation is, but I'll give this a try anyway.
Smooth Operator writes:
That's true, but the rocks do not represent information, they represent themselves.
You keep saying this, but it obviously isn't true. If I express the number 3 using pencil and paper, then that's information. If I instead express the number 3 by dragging rocks into position, then that's information, too. And if the rocks already happen to be in position by luck, then that, too, is information.
Now I understand you think this is wrong, but you need to explain why. So far all you're doing is repeating simple declarations like "That's not information" or "Rocks just represent themselves." Restating your position several different ways is not an explanation.
You didn't explain anything. You just said that he [Gitt] was a nobody in scientific community. Is that an explanation?
I think what you actually need to do here is address my explanation about why Gitt's views have not found any acceptance within the scientific community. You can find that explanation in Message 287.
Saying that he is nobody and doesn't publish in PR articles is not a refutation.
Have you thought this through? How can views never presented to the scientific community become accepted by the scientific community? Gitt's views have no legitimacy within the scientific community. That's not why he's wrong, but that's why you shouldn't be touting Gitt as if his views were widely accepted. They're not.
The reason why Gitt is wrong is because he makes claims he can't support. He claims that meaning is part of information, and that information cannot be created without an intelligence, but he can't quantify his information with meaning, so how would he know? He doesn't. He simply declares that it is so.
He doesn't have to, he is talking in general. To quantify the first three levels of information we can use Dembski's model of CSI. Using this model we can clearly see that mutations do not generate CSI.
Dembski's supposed CSI is just the probability of a protein forming at random from constituent molecules. How is this a measure of information that includes meaning? How is it a measure of information at all?
This is only a theoretical model that does not work that good. The problem is in the noise. There is to much of those who are not as fit as others, so on average the have more chance than the fit ones to reproduce. Therefore effectively shutting down natural selection for beneficial mutations.
You're somehow looking at this backwards. Deleterious mutations is where natural selection really shines versus random selection. According to random selection, a bacterium with a deleterious mutation, even a deadly one, would be as likely to be selected for survival to the next generation as any other bacterium. With random selection, deleterious mutations would quickly accumulate and overwhelm the population, probably wiping it out in short order.
But the type of selection provided by evolution, natural selection, allows bacteria to contribute to the next generation according to fitness. The more beneficial the mutation, the more likely the bacteria is to contribute to the next generation. The less beneficial, the less likely. Because it is much more likely for a mutation to be deleterious than beneficial, it is deleterious mutations that allow natural selection to outperform random selection by so manner orders of magnitude.
Just a moment...
The Crow paper talks about human fitness deteriorating 1-2% in one generation. If natural selection was so great than we would not have this problem. Crow collected data on mutation rates an accumulation of them in the genome. He came to the conclusion that the human genome is deteriorating.
You've managed to completely misinterpret the Crow paper. His concern isn't that natural selection is allowing the accumulation of deleterious mutations. His concern is that modern technologies and medicine have insulated human beings, particular those in western style societies, from the normal effects of natural selection, and so deleterious mutations that in more primitive times would have been removed from the population are now propagating freely. Were we once again exposed to nature in the wild instead of life in environmentally controlled homes with access to modern medical care, those mutations would be again exposed to the forces of natural selection. As Crow himself says:
Crow writes:
It seems clear that for the past few centuries harmful mutations have been accumulating. Why don’t we notice this? If we are like Drosophila, the decrease in viability from mutation accumulation is some 1 or 2% per generation. This is more than compensated for by much more rapid environmental improvements, which are keeping well ahead of any decreased efficiency of selection. How long can we keep this up? Perhaps for a long time, but only if there remains a social order that permits steady environmental improvements. If war or famine force our descendants to return to a stone-age life they will have to contend with all the problems that their stone-age ancestors had plus mutations that have accumulated in the meantime.
Moving on to the Kimura paper:
NCBI
This is discussed in the Kimura paper. See the graph? Notice the darker part of the graph. It's the NNMs. They keep accumulating in the genome.
Neutral mutations both accumulate and are removed. The paper is about how what he calls "selective constraint" allows the neutral mutation model to better describe what is actually observed in nature. "Selective constraint" is his term for natural selection selecting against mutations that cause a decline in fitness, however slight.
That's why I said fitness and new functions are not correlated.
Regardless why you keep saying that fitness and new functions are not correlated, you've got to stop saying it because it makes no sense. It's like saying that any changes in a car's performance is uncorrelated to any changes you make to its engine, transmission, suspension, brakes or aerodynamics.
Evoluton has got to get you new biological functions if you are going to evolve from a bacteria to a man.
And that's precisely what evolution does, one little step at a time.
--Percy

This message is a reply to:
 Message 291 by Smooth Operator, posted 08-08-2009 4:49 PM Smooth Operator has replied

Replies to this message:
 Message 303 by Smooth Operator, posted 08-19-2009 5:28 PM Percy has seen this message but not replied

Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 294 of 315 (518927)
08-09-2009 6:50 PM
Reply to: Message 292 by Smooth Operator
08-08-2009 4:49 PM


I never said that. I said it can be fine tuning.
A phrase with no meaning in biology or informatics. What you seem to be doing is actually conceding the point but insisting we change the words to hide the fact.
There are mutations with beneficial effects which do not cause a net loss in information/functional information, we can call this fine tuning if you like, it doesn't change what it is and it doesn't stop the website you directed us to from being wrong to use such an instance as an example of a loss of information.
They do in vast majority of cases. Even if they don't. Even if they just damage the structure slightly, next few mutations will damage it enough to destroy the function.
You aren't answering the question, the question wasn't, 'Do you think most mutations are detrimental?' It was "If a mutation causes no change in function then please tell me how you measure the change in information involved and determine it to be a net loss?".
When your answer doesn't even make grammatical sense in the context of the question, as yours fails to, then you probably aren't answering the right question.
If you just don't know how you would measure it then why not just say so?
A new house is an ideal. If you throw a rock at it and damage it, it lost some of it structure.
Is this a house you are buying furnished? Let me tell you, my house was a show house when I bought it, an ideal home as it were, and it distinctly benefited from my changing some of the light shades and curtains, yet it is as structurally sound and has all the same lighting and window blocking functionality of before the changes.
TTFN,
WK

This message is a reply to:
 Message 292 by Smooth Operator, posted 08-08-2009 4:49 PM Smooth Operator has replied

Replies to this message:
 Message 304 by Smooth Operator, posted 08-19-2009 5:34 PM Wounded King has not replied

traderdrew
Member (Idle past 5154 days)
Posts: 379
From: Palm Beach, Florida
Joined: 04-27-2009


Message 295 of 315 (519017)
08-10-2009 2:23 PM


Information
Hello everyone and that includes my most toughest debate opponents. I just thought I would post something that might help clear up some misunderstandings aimed at mostly lurkers.
information - 1. the communication of reception of knowledge or intelligence
I would not argue that this definition would represent information inside DNA.
information - 2. the attribute inherent in and communicated by alternative sequences or arrangements of something that produce specific effects.
Information in the second definition would not necessarily require a concious recipient. It can refer to a sequence of characters that produce a specific effect. Software contains information but the computer that reads it is obviously not conscious.
Combinations of nucleotide bases A,C,G, and T inside DNA are arranged in specific orders in order to relay information and they play a part in transcription. The specific effects would result in the completion of certain types of proteins among several other things.

Replies to this message:
 Message 302 by Wounded King, posted 08-19-2009 6:18 AM traderdrew has not replied

Rrhain
Member
Posts: 6351
From: San Diego, CA, USA
Joined: 05-03-2003


Message 296 of 315 (520021)
08-19-2009 4:06 AM
Reply to: Message 238 by Wounded King
08-03-2009 8:27 AM


Wounded King writes:
quote:
I was trying to leave Rrhain some wiggle room since he was saying it was creationist taking things to the courts.
Depends upon which instance you're talking about. Indeed, they have gone off to the school boards, but they have also gone to courts ("balanced treatment" and all that).
For example, John E. Peloza v. Capistrano Unified School District, (1994) 37 F. 3rd 517: Ruling that a teacher's right to freedom of religion was not violated by the district's requirement that evolution be taught in biology class.
There's also Rodney LeVake v Independent School District 656, et al. (Order Granting Defendants' Motion for Summary Judgment and Memorandum, Court File Nr. CX-99-793, District Court for the Third Judicial District of the State of Minnesota [2000]). This case had the teacher claiming discrimination when the school district found his teaching "evidence both for and against the theory" was not part of the curriculum and his religious freedom was not being violated.
So yes, the creationists have moved to the school boards which has resulted in lawsuits originated by those supporting science over religion, but it has also gone the other way with creationists trying to claim that their religious freedom is being trampled by restricting science class to science instruction.

Rrhain

Thank you for your submission to Science. Your paper was reviewed by a jury of seventh graders so that they could look for balance and to allow them to make up their own minds. We are sorry to say that they found your paper "bogus," specifically describing the section on the laboratory work "boring." We regret that we will be unable to publish your work at this time.

This message is a reply to:
 Message 238 by Wounded King, posted 08-03-2009 8:27 AM Wounded King has replied

Replies to this message:
 Message 299 by Wounded King, posted 08-19-2009 5:34 AM Rrhain has not replied

Rrhain
Member
Posts: 6351
From: San Diego, CA, USA
Joined: 05-03-2003


Message 297 of 315 (520026)
08-19-2009 4:51 AM
Reply to: Message 242 by traderdrew
08-03-2009 10:51 AM


traderdrew writes:
quote:
I think he should require (not necessarily demand) that Darwinism needs to be explained on a biochemical level.
But that's just it: They have. They have done the very thing that Behe claims nobody has ever done. In his book, Darwin's Black Box, Behe claims that nobody has ever looked into the biochemical evolution of the blood clot cascade. He even quoted some researchers into it claiming that they had never done so.
But if he had only done a simple check of the literature, he would have seen that not only has the question of the biochemistry of evolution been looked into, but the very people he quoted as having not done the work actually did what he claimed they hadn't. Literally thousands of papers on the biochemistry of evolution had been published at the time Behe came out with his treatise and literally tens of thousands have been written since then but Behe still claims that nobody has ever looked into it.
This was the point of the stack of papers presented to him. He stated in open court that nobody had looked into it so the prosecutor started pulling out paper after paper Behe claimed didn't exist and stacked them up on the witness stand in front of Behe...until he had to eventually complain that he couldn't see over them anymore.
Behe's request that more investigation be done, in and of itself, is reasonable.
What is unreasonable is his continued refusal to acknowledge that his demand for evidence has been provided. Now, this hardly means that everything is known and there is no need to investigate further, but that is not Behe's argument. His claim is not that there is still more work to be done but rather that no work has been done at all.
There is a difference between two mathematicians arguing over whether or not the six millionth digit of pi is a 2 and them arguing over whether or not pi is an integer.
quote:
I don't believe it when someone tells me that Behe doesn't read the journals.
So why does he continue to say that nobody has ever examined the question of the biochemical pathways of evolution?
The cynic in me agrees that Behe has, indeed, read the literature...he's just lying about it.

Rrhain

Thank you for your submission to Science. Your paper was reviewed by a jury of seventh graders so that they could look for balance and to allow them to make up their own minds. We are sorry to say that they found your paper "bogus," specifically describing the section on the laboratory work "boring." We regret that we will be unable to publish your work at this time.

This message is a reply to:
 Message 242 by traderdrew, posted 08-03-2009 10:51 AM traderdrew has not replied

Rrhain
Member
Posts: 6351
From: San Diego, CA, USA
Joined: 05-03-2003


Message 298 of 315 (520031)
08-19-2009 5:34 AM
Reply to: Message 257 by Smooth Operator
08-03-2009 7:52 PM


Smooth Operator responds to me:
quote:
I know it's not the same. That doesn't mean it's new information.
But you can keep repeating this experiment and never stop. By your logic, eventually you'd run out of information. But since we can keep going indefinitely, how does that affect your argument?
quote:
Again, you simply don't get it. New genes do not equal new information.
(*blink!*)
You did not just say that, did you?
Didn't we establish that AB has more information than A? Therefore, how does going from A to AA to AB not equate to "new information"?
quote:
Becasue the loss is gradual.
So why is it we can keep repeating the process indefinitely? How can these bacteria possibly survive when all of their information has been lost?
quote:
Nothing is perfectly neutral.
Huh? A mutation that doesn't affect reproductive success isn't neutral?
Just what is your definition of "neutral"?
quote:
Yes, becasue they will use transposons to produce it again and again.
Huh? If they have transposons, then they haven't lost anything. And the evolution of lactose tolerance after deletion doesn't involve transposons.
Do you even know what a transposon is?
quote:
Nope, it's a designed mechanism that does this.
How can there be a mechanism when there is no gene to digest lactose to be found anywhere in the genome? It was deliberately removed. So are you saying god came down and consciously, deliberately, and purposefully put in a new lactose operon? It was a miracle?
quote:
It has an algorithm that mutates the genome.
Chemistry is a miracle? Because that's how mutations happen: No chemical reaction is ever perfect every single time. Are you saying that this was "designed" by god?
quote:
Because that is biologicaly meaningless.
Huh? Do you not understand how gene cascades form? Duplication and mutation such that the duplicated gene becomes a promotor for the original gene. By your own definition, that is an increase in information because we started with A and we ended with AB.
Since you seem to be backing off, let's try it again:
Which has more information: A or AA?
Which has more information: A or B?
Which has more information: A or AB?
quote:
No new functions are gained by just including one more nucleotide.
Huh? First, why not? Frame shift mutations happen. Second, who was talking about a nucleotide? I was talking about genes.
quote:
Gitt's information is not used for biological functions
Then why did you bring it up? If you're going to use a definition of "information" that you are simply going to reject as inappropriate, why did you mention it?
So let's try it again:
Which has more information: A or AA?
Which has more information: A or B?
Which has more information: A or AB?
quote:
Becasue Shannon's definition of information can't be used for biological functions.
Then why did you bring it up? If you're going to use a definition of "information" that you are simply going to reject as inappropriate, why did you mention it?
So let's try it again:
Which has more information: A or AA?
Which has more information: A or B?
Which has more information: A or AB?

Rrhain

Thank you for your submission to Science. Your paper was reviewed by a jury of seventh graders so that they could look for balance and to allow them to make up their own minds. We are sorry to say that they found your paper "bogus," specifically describing the section on the laboratory work "boring." We regret that we will be unable to publish your work at this time.

This message is a reply to:
 Message 257 by Smooth Operator, posted 08-03-2009 7:52 PM Smooth Operator has replied

Replies to this message:
 Message 305 by Smooth Operator, posted 08-19-2009 5:44 PM Rrhain has not replied

Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 299 of 315 (520032)
08-19-2009 5:34 AM
Reply to: Message 296 by Rrhain
08-19-2009 4:06 AM


I was specifically thinking of the Dover case.
You have to laugh, or cry, when creationists can almost in the same breath claim their 'science' is not religiously motivated and then sue for having their religious freedoms violated when they are told they can't teach it.
The openly religious creationists and the ID crowd need to get their stories straight. I think that is one reason why the school board approach is so flawed, they get the most raving fundamentalists to try and present ID as a non-religious scientific alternative and they just can't do it with a straight face. Mind you I can barely write 'ID is a genuine scientific alternative' without feeling the LOL coming on.
TTFN,
WK

This message is a reply to:
 Message 296 by Rrhain, posted 08-19-2009 4:06 AM Rrhain has not replied

Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 300 of 315 (520033)
08-19-2009 5:35 AM
Reply to: Message 284 by Smooth Operator
08-06-2009 10:22 AM


Gitt's work is based on Shannon.
No.
But it improves it.
No.
But not in a mathematical department, but in general. So there is absolutly no sense to say that his arguments are not valid becasue he didn't use math. He wasn't even supposed to.
But he's pretending that what he's doing is information theory.
It's as though he pretended that his creationist gibberish was Euclidian geometry, and you defended his absurd lie by writing: "Gitt's work is based on Euclid. But it improves it. But not in a geometrical department, but in general. So there is absolutly no sense to say that his arguments are not valid becasue he didn't use geometry. He wasn't even supposed to."

This message is a reply to:
 Message 284 by Smooth Operator, posted 08-06-2009 10:22 AM Smooth Operator has replied

Replies to this message:
 Message 306 by Smooth Operator, posted 08-19-2009 5:45 PM Dr Adequate has replied

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