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Author Topic:   How do "novel" features evolve?
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Posts: 407
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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.

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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Replies to this message:
 Message 305 by Bolder-dash, posted 05-20-2012 5:47 AM zaius137 has not yet responded
 Message 307 by Percy, posted 05-20-2012 7:37 AM zaius137 has not yet responded

Dr Adequate
Posts: 16112
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Message 302 of 314 (662888)
05-20-2012 4:43 AM
Reply to: Message 300 by zaius137
05-20-2012 12:57 AM

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

I don't need to present a reasonable objection to Haldane, because he did not pretend that his work proved creationists right about something for the first time ever.

What I need to do is provide a reasonable objection to the disingenuous creationist halfwits who pretend that he did. And I have done so.

This message is a reply to:
 Message 300 by zaius137, posted 05-20-2012 12:57 AM zaius137 has not yet responded

Dr Adequate
Posts: 16112
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Message 303 of 314 (662889)
05-20-2012 4:48 AM
Reply to: Message 299 by zaius137
05-20-2012 12:28 AM

Re: Mutation rates
(u)=mutation rate (9x10^-9) (60/7x10^9)

I would still like to know why you're dividing 60 by 7x10^9, which is slightly more than twice the actual figure.

this still give a divergence time of 680k generations and 13.6 million years which blows away all of the evolutionist fossil paradigm.

Er ... no. We don't have a fossil known to be the common ancestor of chimps and humans and dated at significantly less than 13.6 million years.

Common descent is nonsense.

Something which has passed actual scientists by, but which is plain to you, an expert in being wrong about things.

This message is a reply to:
 Message 299 by zaius137, posted 05-20-2012 12:28 AM zaius137 has not yet responded

Dr Adequate
Posts: 16112
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Message 304 of 314 (662890)
05-20-2012 4:52 AM
Reply to: Message 298 by zaius137
05-20-2012 12:18 AM

Re: Information
Yes there are two different formulations but they are most certainly relatable.

This is too vague to possess meaning.

Actually, you have not demonstrated any validity to your objections by either citation or any particular principles.

I was kinda relying on the particular principle that Schroedinger didn't own a time machine and could not have been discussing Shannon entropy.

What exactly are you looking for?

Clearly Shannon entropy is not thermodynamic entropy because they are measured in different ways, have different domains, and are expressed in different units.

On the other hand, I have shown a relationship between entropy and information that you emphatically denied existed.

What I have emphatically denied is that thermodynamic entropy is the same as Shannon entropy. You have not shown that they are the same, nor will you.

I do not participate in this forum to win an argument as a matter of fact I learn more by losing the argument…

Only if you're smart enough to notice that you've lost the argument. Otherwise you learn nothing and look like a conceited idiot.

Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 298 by zaius137, posted 05-20-2012 12:18 AM zaius137 has not yet responded

Member (Idle past 2521 days)
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Message 305 of 314 (662893)
05-20-2012 5:47 AM
Reply to: Message 301 by zaius137
05-20-2012 1:20 AM

Re: Information
I have to tell you, that although Dr. A might be wrong about a lot of things, some would probably even fairly say virtually everything, he does happen to be this site's foremost authority on looking like a conceited *****.


Edited by Bolder-dash, : *The asterisks spell out *****, but I just found out Percy's software only allows Dr. A to use the word ***** here, because again, he is an expert at looking like one, so he has a TM of sorts I guess. His is like the ***** King, its his domain.

This message is a reply to:
 Message 301 by zaius137, posted 05-20-2012 1:20 AM zaius137 has not yet responded

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Message 306 of 314 (662896)
05-20-2012 6:44 AM

Bolder-dash Loses Posting Permissions
Because of his history, Bolder-dash is on a very, very short leash here at EvC Forum. I have removed his posting permissions in this forum, the Biological Evolution forum.

EvC Forum Director

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Message 307 of 314 (662901)
05-20-2012 7:37 AM
Reply to: Message 301 by zaius137
05-20-2012 1:20 AM

Re: Information
Hi Zaius,

As I said before, if you understood information theory you'd be explaining it instead of combing the Internet for quotes you can misinterpret to agree with you. Since you did not yourself include any interpretive text for the quote, let me do that for you:

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".

This quote isn't explicit about the direction of the relationship (leaving me puzzled as to why you chose it), but a little thought fills in the missing points. As the amount of information one does not know increases, so does the randomness of the variable one does not know. Randomness increases with increasing message set size, and you learn more from a message from a larger message set than from a smaller one. This is because the uncertainty also has a direct relationship with message set size:

The uncertainty for such a set of n outcomes is defined by

The greater the message set size the greater the uncertainty, and the more our uncertainty is reduced when we receive a message, and therefore the greater the entropy of that message.

It's a direct relationship. For an equiprobable message set of size 2 the probability of each message is .5, the information one does not know is 1 bit, the uncertainty is 1, and the entropy is 1 bit.

For an equiprobable message set of size 4 the probability of each message is .25, the information one does not know is 2 bits, the uncertainty is 2, and the entropy is 2 bits.

For an equiprobable message set of size 8 the probability of each message is .125, the information one does not know is 3 bits, the uncertainty is 3, and the entropy is 3 bits.

Entropy is a measure of our uncertainty about what message we might receive next. The larger the message set, the greater the information we receive in a message. And also the larger the message set, the greater the uncertainty of which message from that set we might receive next, which is the entropy. To understand this better you might consider reading the rest of the article beyond the 2nd paragraph that you quoted. Pay particular attention to the section titled Rationale.

It might also help you to think about the effect of a message on the person receiving it. The person now has more information than he had before, so there are now more messages in his message set, so it would take more bits to communicate the state of this person, so his entropy has risen by the amount of entropy in the message he just received.

If at some point you again feel the urge to provide quotes from the Internet that you're misinterpreting, fight it.

For so long as you fail to care whether your understanding conflicts with the intuitive relationship between information and entropy and even with simple math you will continue to be wrong, not only in your thinking about information theory, but also in any conclusions you reach based upon your misunderstanding, such as the possibility of adding information to the genome.


This message is a reply to:
 Message 301 by zaius137, posted 05-20-2012 1:20 AM zaius137 has not yet responded

Member (Idle past 296 days)
Posts: 20714
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Message 308 of 314 (662943)
05-20-2012 8:29 AM

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.

The early discussion was good, and a few later posts returned to this topic (Wounded King in Message 282), however later discussion turned to information issues, which are a different topic, and one I consider tangential at best to the topic of this thread, and irrelevant at worst.

The number of creationist discussing the topic is discouraging, and so I expect that this issue will continue to be raised, especially as new creationists arrive. It appears that this topic is too advanced for those who do not really understand evolution as a process and confuse it with the theory of evolution.

The issue for creationists is when they will consider the trait to be novel enough -- at what point will they accept that evolution has reached a macro enough level for them to acknowledge that it is significant, without waving it off as "adaptation" or hide behind the "no new information" baggage and denial of evidence, or even denial of their lack of understanding evolution processes.

I would like to be able to say that this tread achieved it's goals, but I can't. Perhaps a second thread that is more focused would work.


Edited by RAZD, : added

we are limited in our ability to understand
by our ability to understand
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Message 309 of 314 (662944)
05-20-2012 9:17 AM

Summary of how "novel" features evolve
There is a population of doggies.

The doggies have puppies.

A few of the puppies are not perfect copies.

Those puppies have webbed feet.

The other puppies think they look funny and call them names.

The environment changes; water levels rise.

The puppies with webbed feet were happy; they played and swam and all hung out together while they laughed at the puppies without webbed feet that couldn't swim real fast all the way from here to there and all the way back again.

The puppies without webbed feet moved to higher ground and they played chase and catch the tail and run around the tree and laughed at the puppies with webbed feet.

Soon there were two different populations, the clean foot puppies and the web foot puppies.

And that is how "novel features" evolve.

Anyone so limited that they can only spell a word one way is severely handicapped!

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

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…

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.

“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.”


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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Message 311 of 314 (663064)
05-21-2012 4:52 AM

I think it worthy of another attempt at this one without getting sidetracked down the rabbit hole of information theory.

It's a reasonable position to take to say something like "fair enough, I accept that natural selection does occur and that it can cause a population to change, but you need now to show me how the genome created those novel features because, until you do, I can say that the genome must have had them to start with."

For example, the peppered moth observations show that selection for a trait can and does occur but doesn't answer the question about how the trait arose in the first place so that it could then be selected for.

Let's have another go?

Life, don't talk to me about life - Marvin the Paranoid Android

Wounded King
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From: Edinburgh, Scotland
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Message 312 of 314 (663081)
05-21-2012 9:54 AM

Too much talking past each other
If the creationists/IDists who have posted on this thread are representative then it seems that there is little if any overlap between what they mean by novel features and what RAZD raised in his OP.

As with the an increase in genetic information a 'novel feature' for a creationist is an abstract thing whose requirements shift as they rule out all the examples for which there is copious evidence. Zaius has just given a few excellent examples here.

A frame shift which produces a novel functional protein from a stretch of DNA with no discernible previous function is dismissed as 'Definitely not new novel functions'. Zaius claims that looking at the evidence supports this but in fact it does no such thing. Ohno characterised the pre-existing sequence from which the nylonase gene was thought to arise as 'very basic ... totally lacking Trp and Asn residues ... not likely to function as an enzyme of any sort'. And yet for this sequence to give rise to an enzyme capable of digesting nylon oligomers does not represent the gain of a novel function according to creationists? I can see that they might make a vague genetic information argument on the basis of the majority of the genetic sequence being present in the right order but to claim that a novel function did not evolve is simply to ignore all the evidence. And to claim this is an examples of 'programmed adaptation' is to make a counter claim for which there is absolutely no evidence.

Claims for 'programmed adaptation' are especially empty since there are multiple experiments in different bacteria where strains lacking nylon metabolising ability have subsequently evolved it through distinct mechanisms (Prijambada et al., 1995; Negoro et al., 2005).

Perhaps if Zaius wishes to discussed the nylon metabolising bacteria in more detail we can take it to an open thread such as 'Is the evidence concerning the Nylon bug being exaggerated'.

As to his comment on the Lenski experiment where oxic Citrate metabolism arose, I am aware of no research which ascribes this mutation to a frame shift. Again it is discounted as not novel enough because anoxic citrate metabolism already existed.

The creationists complain that most of the examples are of duplication and neofunctionalisation seemingly ignoring the fact that these are the mechanisms considered responsible for the vast majority of novel functionality.

They have constructed a crazy argument where any new function based on neofunctionalisation is merely 'adaptation' and any saltational example where a whole novel coding region appears is 'pre-programmed adaptation'. It seems that there is no conceivable evolutionary route to a novel function appearing which they would accept, especially all the ones that we see occurring and have reams of experimental evidence for.

Another common tactic seems to be adding in additional conditions for no good reason, one prime proponent of this method was Bolder-dash who eventually moved to ruling out all evidence from bacterial studies a priori. Zaius seems to be making a similar move by trying to rule out segmental duplications and subsequent mutation as a mechanism responsible for increasing genome size and allowing novel variation and instead insisting we explain it all solely with point mutations.

He also makes an argument complete absent any evidence to support it.

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.

Perhaps he can go to the RAZDs previous Dogs will be Dogs will be ??? thread to substantiate that claim, I would suggest that given what we know about copy number variation (CNV) in mammals including humans his assumption that all dog breeds have genomes of identical size is grossly mistaken. Indeed an important role for CNVs in phenotypic and behavioural variation has already been suggested through comparative studies of dog breed genomes (Nicholas et al., 2009).

Looking back at RAZDs OP I'm not sure the real questions there ever got fully addressed. I think there were some problems with his doggy examples, for instance many wolves do exhibit a substantial degree of webbing between their toes so the extent to which this constitutes a novel feature is highly debatable.

To some extent I think the whole approach suffers from ideally requiring us to have a detailed picture of all the phenotypic variation in the ancestral populations of an organism before we can answer it satisfactorily. While we can feasibly do this in short lived laboratory organisms it is far from feasible when looking at extant populations of something like dogs, especially since we can't really rely on the current extant highly reduced wolf populations to give us a reliable estimate of the variation that was in the grey wolf population prior to domestication thousands of years ago and certainly not of the occasional low frequency variants such a population might have supported.

Perhaps another thread is needed as Tangle suggests. One where discussions of entropy and information are firmly ruled out as off topic.



Dr Adequate
Posts: 16112
Joined: 07-20-2006

Message 313 of 314 (663095)
05-21-2012 11:34 AM

The source of evolutionary novelty, as such, is mutation.

This is obvious; it is practically true by definition. One wonders if even creationists can rely on their natural inborn stupidity in their ceaseless efforts not to understand this, or whether they resort to artificial means such as drink, drugs, or self-inflicted brain damage. One pictures the frustrated religion fanatic sitting alone sobbing in a darkened room ... "I've tried and tried to miss the point, but it's so glaringly obvious" ... (he drinks a bottle of vodka) ... "No, it'sh no ushe, I may not be able to shtand up ... and I shat I've just think myself ... but clearly mutations are the source of evolutionary novelty" ... (he weeps and begins to bang his head against a wall) ... "All I need, all I need is one good big clot in my frontal lobes or shomething ... fucking brain, jusht shtop working!"

I guess that's what creationist websites are for. Somehow they seem to eradicate the victim's capacity for thought while leaving him in possession of his higher motor functions.

Now perhaps this explains their reluctance to discuss the nitty-gritty of genetics, preferring to talk of thermodynamics or information theory or some bizarre melange of the two. These are subjects that they can misunderstand with far greater facility, and have such a tenuous relationship to what is, after all, a very simple question in a completely different field, that even if a creationist did accidentally learn something about these subjects he would not actually have learned anything about evolution.

Take zaius, for example, and his hopeless incomprehension of information theory. Can it even be said to be a barrier to his understanding of evolution? It cannot, because if (which I doubt) we could get him to understand it, he would not actually be able to get any closer to understanding anything about evolution. It's not a barrier that prevents him from understanding evolution, it's a displacement activity that prevents him from trying to understand evolution. While he's wandering around trying to get his befuddled head round information theory, he's not even thinking about evolution, and so the chances of him ever being right about anything are reduced to a safe minimum.

That said, he's pretty darn good at not understanding evolution anyway. He has a fine grasp of how to delicately combine the merely retarded with the completely meaningless in a way that would bring a proud tear to the eye of Henry Morris. When one reads (for example) his nonsense about "adaptation", one sees that not only has he carefully avoided learning the most basic concepts in evolution, but that also he has managed to convince himself that he has acquired such expertise in it as to give smug patronizing lectures on it to others. It is this kind of doublethink, in which ignorance is actively sought and yet profound knowledge is assumed, that produces the most deliciously ridiculous breed of charlatan.

Edited by Dr Adequate, : No reason given.

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Message 314 of 314 (663098)
05-21-2012 11:44 AM

Painting themselves into a corner, AGAIN
Zaius has once again shown us why creationist claims are useless. They claim that novel features must emerge through evolutionary mechanisms in order to produce the biodiversity we see today. So what would happen if we were able to travel back in time to watch every single generation from the first life to modern life, mapping each and every mutation? At every step the creationist would claim that no novel features evolved, ever.

The truth of the matter is that evolution does not need to produce novel features, as defined by creationists, in order to produce the biodiversity we see today. In their attempt to falsify evolution they have moved the goal posts off the field. "Novel feature" is a meaningless term as defined by creationists. "Novel feature" is a hole in the sand where they place their head.

What does evolution need to produce? Heritable phenotypic change. Does it do that? Yep. Mutations produce changes in phenotype that are heritable, and the frequency of these new alleles is controlled by environmental pressures. Whether anyone names this change "novel" or not is completely irrelevant.

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