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Author Topic:   How do "novel" features evolve?
Dr Adequate
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Posts: 16086
Joined: 07-20-2006
Member Rating: 10.0


(2)
Message 286 of 314 (662642)
05-17-2012 3:06 PM
Reply to: Message 284 by zaius137
05-17-2012 2:25 PM


Re: Information
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?


This message is a reply to:
 Message 284 by zaius137, posted 05-17-2012 2:25 PM zaius137 has responded

Replies to this message:
 Message 298 by zaius137, posted 05-20-2012 12:18 AM Dr Adequate has responded

  
Dr Adequate
Member
Posts: 16086
Joined: 07-20-2006
Member Rating: 10.0


Message 287 of 314 (662643)
05-17-2012 3:12 PM
Reply to: Message 285 by zaius137
05-17-2012 3:01 PM


Re: The origin of novel genes, a related issue.
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?


This message is a reply to:
 Message 285 by zaius137, posted 05-17-2012 3:01 PM zaius137 has responded

Replies to this message:
 Message 292 by zaius137, posted 05-17-2012 6:43 PM Dr Adequate has responded

  
Wounded King
Member (Idle past 2174 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 288 of 314 (662653)
05-17-2012 5:49 PM
Reply to: Message 285 by zaius137
05-17-2012 3:01 PM


Re: The origin of novel genes, a related issue.
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


This message is a reply to:
 Message 285 by zaius137, posted 05-17-2012 3:01 PM zaius137 has responded

Replies to this message:
 Message 290 by Taq, posted 05-17-2012 6:14 PM Wounded King has acknowledged this reply
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zaius137
Member (Idle past 1489 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 (http://www.genetics.org/content/156/1/297.full) 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.

http://www.brighthub.com/...nce/genetics/articles/34219.aspx


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 responded

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

  
Taq
Member
Posts: 7673
Joined: 03-06-2009
Member Rating: 2.8


Message 290 of 314 (662660)
05-17-2012 6:14 PM
Reply to: Message 288 by Wounded King
05-17-2012 5:49 PM


Re: The origin of novel genes, a related issue.
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:
Haldane stated at the time of publication "I am quite aware that my conclusions will probably need drastic revision", and subsequent corrected calculations found that the cost disappears. He had made an invalid simplifying assumption which negated his assumption of constant population size, and had also incorrectly assumed that two mutations would take twice as long to reach fixation as one, while sexual recombination means that two can be selected simultaneously so that both reach fixation more quickly. The creationist claim is based on further errors and invalid assumptions.
http://en.wikipedia.org/wiki/Haldane's_dilemma


This message is a reply to:
 Message 288 by Wounded King, posted 05-17-2012 5:49 PM Wounded King has acknowledged this reply

  
zaius137
Member (Idle past 1489 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 acknowledged this reply

Replies to this message:
 Message 296 by Dr Adequate, posted 05-17-2012 9:09 PM zaius137 has responded
 Message 297 by Taq, posted 05-18-2012 4:32 PM zaius137 has not yet responded

  
zaius137
Member (Idle past 1489 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:
 Message 287 by Dr Adequate, posted 05-17-2012 3:12 PM Dr Adequate has responded

Replies to this message:
 Message 295 by Dr Adequate, posted 05-17-2012 8:20 PM zaius137 has not yet responded

  
Wounded King
Member (Idle past 2174 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 293 of 314 (662676)
05-17-2012 7:47 PM
Reply to: Message 289 by zaius137
05-17-2012 6:06 PM


Re: Mutation rates
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


This message is a reply to:
 Message 289 by zaius137, posted 05-17-2012 6:06 PM zaius137 has responded

Replies to this message:
 Message 299 by zaius137, posted 05-20-2012 12:28 AM Wounded King has acknowledged this reply

    
Percy
Member
Posts: 18310
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.9


Message 294 of 314 (662678)
05-17-2012 8:18 PM
Reply to: Message 284 by zaius137
05-17-2012 2:25 PM


Re: Information
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.


This message is a reply to:
 Message 284 by zaius137, posted 05-17-2012 2:25 PM zaius137 has responded

Replies to this message:
 Message 301 by zaius137, posted 05-20-2012 1:20 AM Percy has responded

    
Dr Adequate
Member
Posts: 16086
Joined: 07-20-2006
Member Rating: 10.0


Message 295 of 314 (662679)
05-17-2012 8:20 PM
Reply to: Message 292 by zaius137
05-17-2012 6:43 PM


Re: The origin of novel genes, a related issue.
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.


This message is a reply to:
 Message 292 by zaius137, posted 05-17-2012 6:43 PM zaius137 has not yet responded

  
Dr Adequate
Member
Posts: 16086
Joined: 07-20-2006
Member Rating: 10.0


Message 296 of 314 (662682)
05-17-2012 9:09 PM
Reply to: Message 291 by zaius137
05-17-2012 6:27 PM


Re: The origin of novel genes, a related issue.
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."


This message is a reply to:
 Message 291 by zaius137, posted 05-17-2012 6:27 PM zaius137 has responded

Replies to this message:
 Message 300 by zaius137, posted 05-20-2012 12:57 AM Dr Adequate has responded

  
Taq
Member
Posts: 7673
Joined: 03-06-2009
Member Rating: 2.8


Message 297 of 314 (662775)
05-18-2012 4:32 PM
Reply to: Message 291 by zaius137
05-17-2012 6:27 PM


Re: The origin of novel genes, a related issue.
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.


This message is a reply to:
 Message 291 by zaius137, posted 05-17-2012 6:27 PM zaius137 has not yet responded

  
zaius137
Member (Idle past 1489 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…

http://www.chemeurope.com/...opedia/Information_entropy.html


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 responded

Replies to this message:
 Message 304 by Dr Adequate, posted 05-20-2012 4:52 AM zaius137 has not yet responded

  
zaius137
Member (Idle past 1489 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.


This message is a reply to:
 Message 293 by Wounded King, posted 05-17-2012 7:47 PM Wounded King has acknowledged this reply

Replies to this message:
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zaius137
Member (Idle past 1489 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.


This message is a reply to:
 Message 296 by Dr Adequate, posted 05-17-2012 9:09 PM Dr Adequate has responded

Replies to this message:
 Message 302 by Dr Adequate, posted 05-20-2012 4:43 AM zaius137 has not yet responded

  
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