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Author Topic:   How do "novel" features evolve?
zaius137
Member (Idle past 3436 days)
Posts: 407
Joined: 05-08-2012


Message 274 of 314 (662466)
05-16-2012 12:29 AM
Reply to: Message 271 by PaulK
05-15-2012 2:06 PM


Re: Information
PaulK my friend,
I am not a mathematician by any sense of the word but believe that it is not that the unfair coin posses less information but my understanding is that the unfair coin is more predictable. Therefore, it takes less information to transmit the result of the toss. I have received some criticism that I am using the term information incorrectly, when I refer to the message possessing more information. This criticism may be justified so I have been using the term negentropy instead.
Anyway, I am trying to express that a more predictable message would posses less entropy thus the transmission of that message would require less bits.
What is your opinion?

This message is a reply to:
 Message 271 by PaulK, posted 05-15-2012 2:06 PM PaulK has replied

Replies to this message:
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zaius137
Member (Idle past 3436 days)
Posts: 407
Joined: 05-08-2012


Message 275 of 314 (662470)
05-16-2012 12:52 AM
Reply to: Message 1 by RAZD
03-08-2012 10:47 PM


Re: what is novel?
RAZD my friend,
Entropy is not my favorite subject so I will try and get back onto the theme of your original post How do novel features evolve?
I will ask if novel features can evolve at all, given that there are not enough mutations to create them. Let me ask the following question
Are there enough random mutations to create new innovative features between humans and chimps?
To illustrate my point, I will calculate de novo the time needed for the supposed Pan Human divergence with current findings of mutation rate and divergence between chimp and human genes.
Commonly the date accepted by evolutionists is 5 million years. I will show that 5 million years is impossibly short given the actual evidence.
The formula comes from a paper by Michael W. Nachman and Susan L. Crowell and was originally used to estimate the needed mutation rate per generation to change a common ancestor hominid into a human in 5 million years. I believe the formulation arrived at 175 mutations per generation but there has been an empirical adjustment to the calculated rate of only 60 mutations per generation (about 1/3). In addition, the mutation divergence of autosomal Pseudogenes has been raised slightly too about 3% between chimps and humans.
The formula k= 2(u)t+4Ne(u) (variables defied below)
My 3% is form
quote:
... on closer inspection we differ by 1.2% in the functional genes that code for proteins. And we also differ by about 3% in the non-coding DNA regions, so called "junk DNA" - although this phrase seems to be losing meaning as some of these regions regulate genes and possess as yet unknown functions. So overall we can say that chimp and human DNA is about 96% identical - which is still very close. If you were to lay both genomes out side by side you would see that base for base they are 96% similar.
https://www.brighthub.com/science/genetics/articles/34219/
60 mutations per generation from:
http://www.geneticarchaeology.com/...d_of_human_mutation.asp
The Average Human Has 60 New Genetic Mutations - Slashdot
I will work the equation in reverse inserting the known mutation rate per generation in humans and the newer pseudogene divergence.
t= .5(k/u-4Ne)
t= number of generations since divergence (Generation =20 years)
k= percentage of sequence divergence Estimated at 3%
Ne= effective size of population (10^4)
(u)=mutation rate (9x10^-9) (60/7x10^9)
From Estimate of the Mutation Rate per Nucleotide in Humans | Genetics | Oxford Academic
(t) In generations is 1.65 million or 33 million years since the human chimp divergence
In other words, new evidence in genetic divergence between chimps and humans and the measured mutation rate in humans has pushed the possible divergence back to 33 million years. You cannot change a monkey into a man.
Edited by zaius137, : No reason given.

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zaius137
Member (Idle past 3436 days)
Posts: 407
Joined: 05-08-2012


Message 284 of 314 (662635)
05-17-2012 2:25 PM
Reply to: Message 279 by Percy
05-16-2012 7:41 AM


Re: Information
I rather not dwell on entropy but I cannot let you go on thinking I have no point.
My point is that lower entropy implies that the message has more information. I can see now that my original argument posed no direct explanation of a correlation. Let me make another attempt at that point by appealing to two thought experiments (Maxwell’s demon and Szilard’s engine).
These two thought experiments relate how information can lower entropy.
quote:
Szilard's engine
A neat physical thought-experiment demonstrating how just the possession of information might in principle have thermodynamic consequences was established in 1929 by Le Szilrd, in a refinement of the famous Maxwell's demon scenario.
Let me go a bit further with this thought and mention a direct mathematical correlation between entropy and information by Brillouin. It is a refinement on the negentropy/information idea.
quote:
I = K ln P
where I denotes information, K is a constant, and P is the probability of the outcome. Brillouin reasons that with these types of probability arguments, it enables one to solve the problem of Maxwell’s demon and to show a very direct connection between information and entropy and that the thermodynamic entropy measures the lack of information about a physical system. Moreover, according to Brillouin, whenever an experiment is performed in the laboratory, it is paid for by an increase in entropy, and a generalized Carnot principle states that the price paid in increase of entropy must always be larger than the amount of information gained. Information, according to Brillouin, corresponds to negative entropy or negentropy, a term he coined.
So tell me again how information does not correlate inversely to entropy? Probability of the message increases, information in the message increases, entropy decreases.

This message is a reply to:
 Message 279 by Percy, posted 05-16-2012 7:41 AM Percy has replied

Replies to this message:
 Message 286 by Dr Adequate, posted 05-17-2012 3:06 PM zaius137 has replied
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zaius137
Member (Idle past 3436 days)
Posts: 407
Joined: 05-08-2012


Message 285 of 314 (662641)
05-17-2012 3:01 PM
Reply to: Message 282 by Wounded King
05-16-2012 12:09 PM


Re: The origin of novel genes, a related issue.
Hi again Wounded King,
I found this paper interesting in that it relies implicitly on the pre existence of the genetic code. So how did the duplicated gene sequence occur in the first place given no original gene sequence?
quote:
Based on cytological observations of chromosomal duplications, Haldane (1933) and Muller (1935) already hypothesized in the 1930s that new gene functions may emerge from refashioned copies of old genes, highlighting for the first time the potential importance of gene duplication for the process of new gene origination.
Origins, evolution, and phenotypic impact of new genes - PMC
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? This is known as Haldane’s dilemma.
This paper only speaks from the assumption that common descent is unquestionably correct. Nothing is further from the truth.
I found this paper rather thin in explanations. However, I thank you for the citation.

This message is a reply to:
 Message 282 by Wounded King, posted 05-16-2012 12:09 PM Wounded King has replied

Replies to this message:
 Message 287 by Dr Adequate, posted 05-17-2012 3:12 PM zaius137 has replied
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zaius137
Member (Idle past 3436 days)
Posts: 407
Joined: 05-08-2012


Message 289 of 314 (662659)
05-17-2012 6:06 PM
Reply to: Message 281 by Wounded King
05-16-2012 11:13 AM


Re: Mutation rates
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:
t= number of generations 250k (Generation =20 years) (5x10^6/20)
(from 5 million years)
k= as variable
Ne= effective size of population ~10^4
(u)=mutation rate 2.5x10^-8 or 175 new mutations/generation (175/7x10^9)
Please note the units for mutation rate.
k= 2ut + 4 Neu
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:
... on closer inspection we differ by 1.2% in the functional genes that code for proteins. And we also differ by about 3% in the non-coding DNA regions, so called "junk DNA" - although this phrase seems to be losing meaning as some of these regions regulate genes and possess as yet unknown functions. So overall we can say that chimp and human DNA is about 96% identical - which is still very close. If you were to lay both genomes out side by side you would see that base for base they are 96% similar.
https://www.brighthub.com/science/genetics/articles/34219/
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.

This message is a reply to:
 Message 281 by Wounded King, posted 05-16-2012 11:13 AM Wounded King has replied

Replies to this message:
 Message 293 by Wounded King, posted 05-17-2012 7:47 PM zaius137 has replied

  
zaius137
Member (Idle past 3436 days)
Posts: 407
Joined: 05-08-2012


Message 291 of 314 (662662)
05-17-2012 6:27 PM
Reply to: Message 288 by Wounded King
05-17-2012 5:49 PM


Re: The origin of novel genes, a related issue.
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.
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 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.
Thanks for the citations

This message is a reply to:
 Message 288 by Wounded King, posted 05-17-2012 5:49 PM Wounded King has seen this message but not replied

Replies to this message:
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zaius137
Member (Idle past 3436 days)
Posts: 407
Joined: 05-08-2012


Message 292 of 314 (662667)
05-17-2012 6:43 PM
Reply to: Message 287 by Dr Adequate
05-17-2012 3:12 PM


Re: The origin of novel genes, a related issue.
Dr. Adaquate
Do you have no shame?
You the MAN. Oops this is not politically correct. You the self empowered generic individual.

This message is a reply to:
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zaius137
Member (Idle past 3436 days)
Posts: 407
Joined: 05-08-2012


Message 298 of 314 (662882)
05-20-2012 12:18 AM
Reply to: Message 286 by Dr Adequate
05-17-2012 3:06 PM


Re: Information
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:
See Relationship to thermodynamic entropy on this page
Information_entropy
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.

This message is a reply to:
 Message 286 by Dr Adequate, posted 05-17-2012 3:06 PM Dr Adequate has replied

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zaius137
Member (Idle past 3436 days)
Posts: 407
Joined: 05-08-2012


Message 299 of 314 (662883)
05-20-2012 12:28 AM
Reply to: Message 293 by Wounded King
05-17-2012 7:47 PM


Re: Mutation rates
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 3436 days)
Posts: 407
Joined: 05-08-2012


Message 300 of 314 (662884)
05-20-2012 12:57 AM
Reply to: Message 296 by Dr Adequate
05-17-2012 9:09 PM


Re: The origin of novel genes, a related issue.
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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zaius137
Member (Idle past 3436 days)
Posts: 407
Joined: 05-08-2012


Message 301 of 314 (662885)
05-20-2012 1:20 AM
Reply to: Message 294 by Percy
05-17-2012 8:18 PM


Re: Information
Percy my friend
You seem to like the wiki so here is something to chew on.
quote:
Equivalently, the Shannon entropy is a measure of the average information content one is missing when one does not know the value of the random variable. The concept was introduced by Claude E. Shannon in his 1948 paper "A Mathematical Theory of Communication"
What is missing, is less, if it is less random or has more information in it (the random variable).
Your friend Zaius

This message is a reply to:
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zaius137
Member (Idle past 3436 days)
Posts: 407
Joined: 05-08-2012


Message 310 of 314 (663058)
05-21-2012 2:35 AM


Summation
Well done RAZD
I started this thread to discuss how novel features or traits evolve, with some examples that raise the question of when a new trait is considered novel.
From a creationist standpoint, we know that the evolutionist has always confused new novel traits arising with the process of adaptation.
New novel features beg the question how point mutations lengthen genomes to code for these new novel traits. The very best the evolutionist has been able to come up with is gene duplications that incorporate point mutations to produce novel gene segments. The question the evolutionist has never answered is where the original gene sequence came from in the first place. The case of dog diversity is a perfect example of what I am talking about; all dogs have the same sized genome, it has not grown in size even when new traits appear.
About a previous post
Concerning mutations in dogs, I will ask what kind of point mutation would occur in dogs to give them webbed feet and why webbed feet would get fixed in a population not under immediate selection for webbed feet. Just about, everyone can make up convoluted scenarios that sound reasonable but evolution always fails in the light of reason and empirical findings.
I brought up two cases that are examples posed by evolutionists of new traits arising in E. coli and Flavobacterium. As I pointed out that both these cases were examples of DNA open reading frame shifts causing E. coli to metabolize citrate and the Flavobacterium to us nylon as a food source. Definitely not new novel functions if you examine the actual evidence.
I would also like to bring up a contemporary of Darwin who observed the same evidence in nature that Darwin did but came to a very different conclusion. Concerning Edward Blyth
quote:
Thus with Blyth, natural selection is a homeostatic mechanism to prevent change. Blyth was not the only one to use this argument.4 Yet Darwin never explicitly addressed the possibility that natural selection could thwart evolution and he presented natural selection as a developmental mechanism.
Again, I will ask the evolutionist if no new spontaneous segments of genes arise in genomes how are species gaining unique sequences of DNA and novel new functions. By unique new segments, I am not referring to genome duplications.
quote:
Evolution's mutation mechanism does not explain how growth of a genome is possible. How can point mutations create new chromosomes or lengthen a strand of DNA? It is interesting to note that, in all of the selective breeding in dogs, there has been no change to the basic dog genome. All breeds of dog can still mate with one another. People have not seen any increase in dog's DNA, but have simply selected different genes from the existing dog gene pool to create the different breeds.
Question 1: How Does Evolution Add Information? - How Evolution Works | HowStuffWorks
Evolutionists have no evidence that new novel traits have ever arisen besides the fact that the genome is built to adapt.
Edited by zaius137, : No reason given.

  
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