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Member (Idle past 1653 days) Posts: 20714 From: the other end of the sidewalk Joined: |
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Author | Topic: How do "novel" features evolve? | |||||||||||||||||||||||||||||||||||||||
Dr Adequate Member Posts: 16113 Joined:
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I rather not dwell on entropy ... I can see why.
So tell me again how information does not correlate inversely to entropy? Shannon entropy is different from thermodynamic entropy. They are not the same. They are different.
Probability of the message increases, information in the message increases ... No it doesn't. How many times does this need to be explained to you? If it is 100% certain that the message I am about to receive will consist of the word "YES", then that message contains no information. Because I learn nothing whatsoever by receiving it. Because I already knew what it would say. How hard can this be to understand? How fucking hard can this be to understand? How obvious does an idea need to be before a creationist can understand it? Really, how simple does it need to be? If we tried to say to a creationist: "The cat sat on the mat", would you guys be all: "So you're saying the mat is on top of the dog, right? Only that's how I understand it"?
What the fuck is wrong with you people?
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Dr Adequate Member Posts: 16113 Joined: |
Remember Haldane’s fixation of new functional genes only happens one every 300 generations. This would provide only about 1700 new beneficial functions fixed in humans since the Pan Human divergence! Are there only about 1700 functional mutations between humans and chimps? Quite possibly. Do you have a scrap of a shred of a shard of a scintilla of an iota of actual evidence to the contrary?
This is known as Haldane’s dilemma. And for the benefit of creationists, I should explain that Haldane's dilemma is a real actual thing in real biology as practiced by real biologists. Only some of you seem to think that "Haldane's dilemma" are two magic words that you can recite which will make every fact that you hate about biology magically disappear. You think this because you are grossly and repugnantly ignorant of the very subject that you are pretending to know something about. Do you have no shame?
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Wounded King Member (Idle past 281 days) Posts: 4149 From: Cincinnati, Ohio, USA Joined: |
So how did the duplicated gene sequence occur in the first place given no original gene sequence? It is a bit hard to parse this question. Do you mean how did the original sequence from which the duplicate arose originate? As it stands the question seems nonsensical since the duplicated gene sequences clearly did have original gene sequences. As for Haldane's dilemma there is a substantial body of literature stretching back decades showing that many exceptions to Haldane's underlying assumptions can be found in actual biological populations, (Grant and Flake, 1974). Population genetics has moved on considerably in the half century or so since Haldane first published on selection costs. Haldane's 300 generations was based on a very specific model with particular assumptions backing it, to assume it can be used generally as you have is frankly ridiculous.
I found this paper rather thin in explanations. However, I thank you for the citation. Well it was a review paper, there are plenty of citations if you are keen to dig into the details of a particular mechanism. TTFN, WK
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zaius137 Member (Idle past 3657 days) Posts: 407 Joined: |
Wounded King my friend,
To set your mind at ease about my calculation I went back to the paper I cited (Estimate of the Mutation Rate per Nucleotide in Humans | Genetics | Oxford Academic) and went threw one of there calculations comparing results. I did the following:
quote: I got a (k) value (or average autosomal pseudogene difference) of 1.26%; but at this point I will claim a higher value for (k) but only about 3%.... This seems to line up with the findings of that older paper (.6% to 2.6%) and new research. My 3% again is form
quote: Sorry to say this but the junk DNA has been reevaluated upward. Some articles are even suggesting a greater divergence. Alos it is important to note that in the Chimp genome project approximately (.7Gb) of that genome failed to align at all. If researchers fail to figure out how to align the extra .7Gb the total divergence would add up to an additional 22.6% divergence.
I don't really see how this is much more relevant to the topic. Especially since the calculations are based on what are considered neutral regions of the genome that we wouldn't expect to be where we would find adaptive features, novel or otherwise. Without knowing what the mutation rate for adaptive substitutions is and the divergence based on adapative sites you seem to be addressing another question entirely, namely whether there is enough time between the human-chimp divergence to account for the genetic divergence we see based on current estimates of mutation rates. I don't see where novel features come into it, especially if we accept that novel features including protein coding genes can arise de novo from single step mutations a phenomenon for which there is now considerable evidence in many species including 60 such putative genes in humans (Wu et al., 2011). So you disagree with Michael W. Nachman and Susan L. Crowell? Funny how the best authorities in the evolutionary field are discarded if there is any kind of problem showing common descent could be wrong. The evolutionist has a lot of work to do.
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Taq Member Posts: 10293 Joined: Member Rating: 7.4 |
As for Haldane's dilemma there is a substantial body of literature stretching back decades showing that many exceptions to Haldane's underlying assumptions can be found in actual biological populations, (Grant and Flake, 1974). Population genetics has moved on considerably in the half century or so since Haldane first published on selection costs.
To put it another way, Haldane's Dilemma is no longer a Dilemma. Wiki has a nice paragraph on it:
quote:
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zaius137 Member (Idle past 3657 days) Posts: 407 Joined: |
Wounded King my friend,
It is a bit hard to parse this question. Do you mean how did the original sequence from which the duplicate arose originate? As it stands the question seems nonsensical since the duplicated gene sequences clearly did have original gene sequences. So, where did they originally come from? A classic chicken or egg scenario.
As for Haldane's dilemma there is a substantial body of literature stretching back decades showing that many exceptions to Haldane's underlying assumptions can be found in actual biological populations, (Grant and Flake, 1974). Population genetics has moved on considerably in the half century or so since Haldane first published on selection costs.
I like that Grant and Flake funny. I read this and it is nothing but a hand wave (there is no real rebuttal to Haldane’s calculations). I used Haldane because he is an authority, criticized but not disproved, he still stands in the field. Maybe you would like to discuss Nunney’s simulation.Haldane's 300 generations was based on a very specific model with particular assumptions backing it, to assume it can be used generally as you have is frankly ridiculous. Thanks for the citations
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zaius137 Member (Idle past 3657 days) Posts: 407 Joined: |
Dr. Adaquate
Do you have no shame? You the MAN. Oops this is not politically correct. You the self empowered generic individual.
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Wounded King Member (Idle past 281 days) Posts: 4149 From: Cincinnati, Ohio, USA Joined: |
My 3% again is form Yes, its from a web article which provides no reference so we basically have no idea what research the figure comes from or what data it was derived from and certainly no indication that it refers to autosomal pseudogenes, which I think I pointed out quite clearly previously.
Sorry to say this but the junk DNA has been reevaluated upward. Some articles are even suggesting a greater divergence. Once again you fail to address the actual criticism I made of your position and just double down on insisting your approach is appropriate. If a large proportion of this divergence is due to indel's, and if you read the chimp genome consortium papers (2005) you'll know that it is, then they represent the same issue I already highlighted with regard to the appropriateness of divergence due to length mutations in determining divergence times.
So you disagree with Michael W. Nachman and Susan L. Crowell? No, I disagree with you. Nachman and Crowell made a specific estimate based on divergences from a specific set of pseudogenes chosen as representing neutral genetic regions and with clear well aligned orthologues. You instead are taking a random number you found on the internet that is no more specific in what it applies to than 'junk DNA' and expecting us to give it equal weight. I point out reasons why this is suspect, especially if that divergence value is substantially based on length mutations, and you just ignore the objections and rely on an appeal to authority despite the authorities in question not making the claims you seem to wish to use them to defend. Did Nachman and Crowell claim they were looking for a rate to explain novel adaptive mutations? No they didn't. If you care to actually make some effort and show where I am disagreeing with Nachman and Crowll then please do so. TTFN, WK
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Percy Member Posts: 22929 From: New Hampshire Joined: Member Rating: 7.2 |
zaius137 writes: I rather not dwell on entropy but I cannot let you go on thinking I have no point. If you'd rather not dwell on entropy then stop being wrong about it, which you continued doing in this message, demonstrating that you do indeed have no point, but even more importantly that you have little comprehension or intuitive feel for the subject
My point is that lower entropy implies that the message has more information. You have a stunning lack of interest about resolving the conflict between what you believe and what the math of information theory says.
These two thought experiments relate how information can lower entropy. I'll address this in a moment, but first it's important that you recognize that this isn't what you were originally wrong about. You originally asserted that the greater the information the less the entropy. This was wrong. You next asserted that static information and transmitted information are different, and that in one the relationship between information and entropy was direct, in the other inverse. This, too, was wrong. You've now changed realms from information theory to thermodynamics and quantum theory. You've also changed questions from, "How much information and entropy is there?" to "How much entropy will it cost to gain information about a physical system?" This is the 2nd Law of Thermodynamics which states that the entropy of any closed system can only increase. If one does work in order to gain information then the cost to you in entropy will always be greater than the information gained. In other words, if you did work that gained you 2-bits of information with an entropy of 2, then you must have exerted work costing more than 2 units of entropy in order to gain that information. This entropy cost is what Brillioun called negentropy because it is what you have to give up in order to gain information. But the more information you want to gain the more entropy you have to give up. And the more information your gain, the more entropy that information has, though that entropy is less than the entropy you gave up in order to gain the information (2nd Law of Thermodynamics again). It's a positive relationship. If you really understood this you'd be explaining it instead of combing the Internet for quotes you can misinterpret to agree with you. I suggest you read the Wikipedia article on information theory, it's actually pretty good and pretty simple, and once you can explain your viewpoint without blatantly contradicting the simple math of information theory you come back here and see if you still believe that information and entropy are inversely related. --Percy Edited by Percy, : Typo.
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Dr Adequate Member Posts: 16113 Joined: |
You know where I asked:
Do you have a scrap of a shred of a shard of a scintilla of an iota of actual evidence ... Maybe you could address yourself to that instead of writing words at random.
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Dr Adequate Member Posts: 16113 Joined: |
I used Haldane because he is an authority ... Splendid. Then you will please note that he himself did not think that his work magically proved creationists right about everything. Or, indeed, anything. Perhaps this is because he knew something about his work that you don't, like what it was. You can find his original paper here. Note the complete absence of the words: "And so this proves that creationists are right about something, albeit in some way that they will never adequately be able to explain."
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Taq Member Posts: 10293 Joined: Member Rating: 7.4 |
I used Haldane because he is an authority, criticized but not disproved, he still stands in the field. His dilemma is irrelevant to how species evolve in the real world.
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zaius137 Member (Idle past 3657 days) Posts: 407 Joined: |
Dr. Adequate my friend
Shannon entropy is different from thermodynamic entropy. They are not the same. They are different.
Yes there are two different formulations but they are most certainly relatable. Consider Gibbs algorithm and resemblance to Gibbs entropy.
quote: Actually, you have not demonstrated any validity to your objections by either citation or any particular principles. On the other hand, I have shown a relationship between entropy and information that you emphatically denied existed. I do not participate in this forum to win an argument as a matter of fact I learn more by losing the argument try putting some substance behind those objections.
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zaius137 Member (Idle past 3657 days) Posts: 407 Joined: |
Wounded King my friend,
My 3% again is form
Yes, its from a web article which provides no reference so we basically have no idea what research the figure comes from or what data it was derived from and certainly no indication that it refers to autosomal pseudogenes, which I think I pointed out quite clearly previously. Here is the punch line If you disagree with the 3% fine here is the calculation again using 1.26% (argue with that figure all you want but your argument would be with Nachman). t= number of generations since divergence (Generation =20 years)k= percentage of sequence divergence Estimated at 1.26% Ne= effective size of population (10^4) (u)=mutation rate (9x10^-9) (60/7x10^9) this still give a divergence time of 680k generations and 13.6 million years which blows away all of the evolutionist fossil paradigm. Common descent is nonsense.
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zaius137 Member (Idle past 3657 days) Posts: 407 Joined: |
Dr. Adequate my friend
Splendid. Then you will please note that he himself did not think that his work magically proved creationists right about everything. Or, indeed, anything. Perhaps this is because he knew something about his work that you don't, like what it was. In 1993 Walter ReMine’s, book "The Biotic Message, Haldane’s calculations were upheld and verified. The evolutionist has never presented a reasonable objection to Haldane.
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