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Author Topic:   Evolving New Information
Percy
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Posts: 18492
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.8


Message 1 of 458 (507055)
05-01-2009 8:57 AM


This is a continuation of a digression that arose in the A Designer Consistent with the Physical Evidence thread concerning how mutation produces new information. What follows is just a copy of my Message 324.

--Percy


NanoGecko writes:

It is just as well that the DNA contains so many base pairs of coded information, and that there is a safety mechanism in that usually both parents need to have the copying error (mutation) before the mutation will express itself in the offspring.


Whether any gene is expressed is a function of many things, the one we're most familiar with being the dominant/recessive characteristic. In sexual species a mutation does not need to be present in both parents in order to be expressed in the offspring, and so it is possible for a mutation to express itself in the first generation of its appearance. And of course in non-sexual species this isn't an issue.

Your analogy is only about a mixing of genetic information via the amazing process of sexual reproduction to produce a variety of offspring outcomes.

Actually, it wasn't an analogy, I didn't specify the type of reproduction, and it was an example of a single mutation, not allele mixing such as would occur with sexual reproduction. If it helps, it is simplest to think of the example organism as a sighted asexual species with eye color.

You weren't specific about what portions of my example you took issue with, so help me figure this out. Our organism has three alleles for eye color:

  • GGAACG (green eyes)
  • GGAACA (blue eyes)
  • GGCACG (yellow eyes)

Since there are three messages in the message set for this gene, the amount of information it can communicate is log23 = 1.585 bits. This is just straightforward information theory, I'm just setting the table right now, there shouldn't be anything here to take issue with. I think this is what you prefer to call complex specified information, and I'll attempt to accommodate you.

Now we look at a single reproductive event where an organism with the allele for yellow eyes (CGCACG) produces an offspring with a mutation in this gene so that it is now CGCACA, and the offspring has brown eyes. Our message set has now become:

  • GGAACG (green eyes)
  • GGAACA (blue eyes)
  • GGCACG (yellow eyes)
  • GGCACA (brown eyes)

There are now four messages in the message set for this gene, and the amount of information it can communicate is log24 = 2 bits, an increase of .415 bits.

You had several objections to this. One is that the mutation for brown eyes is polymorphic, and I have to completely agree. Having multiple alleles for a gene is the very definition of polymorphism, and increasing the number of alleles is, at heart, the way that mutation increases the amount of information in a genome. You later say:

The NEW information that I am talking about is the ACTUAL NEW INFORMATION THAT IS REQUIRED TO HAVE OCCURRED by those that believe in the evolutionary fairy story.

So you're asking us to describe the type of new information that is required by evolution to rpovide new functions, and my mutation example is exactly that. Mutations are ultimately how evolution provides new function, and I provided an example of a mutation providing a new function, and showed how from an information theoretic perspective that it represented new information. If you think it doesn't provide new information then you have to explain how the message set growing from 3 messages via mutation to become 4 is not an increase in information. log24 - log23 = +.415 is the simple math that you have to address.

Another of your objections dealt with complex specified information:

BUT they do NOT constitute a coded increase in ordered complexity in the genetic code...

My example began with an organism with an eye-color gene with three alleles, and you call this complex specified information (you actually used the term "ordered complexity", but hopefully this is a synonym). I then said there was a mutation that added an allele, and you're saying that the added allele is not complex specified information.

But what if I had instead begun my example by saying that the organism originally had four alleles for eye color like this:

  • GGAACG (green eyes)
  • GGAACA (blue eyes)
  • GGCACG (yellow eyes)
  • GGCACA (brown eyes)

You would have said this is the complex specified information for that gene and had no problem with it, just as you did when I began my example with a three-allele gene. So if the allele for brown eyes is complex specified information when it is part of the original genome, how is it not complex specified information when it arises through mutation?

--Percy

Edited by Percy, : "complex specified complexity" => "complex specified information"


Replies to this message:
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 Message 42 by LucyTheApe, posted 05-22-2009 9:45 AM Percy has responded
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AdminModulous
Administrator (Idle past 276 days)
Posts: 897
Joined: 03-02-2006


Message 2 of 458 (507057)
05-01-2009 9:18 AM


Thread moved here from the Proposed New Topics forum.
    
Peepul
Member (Idle past 3189 days)
Posts: 206
Joined: 03-13-2009


Message 3 of 458 (507059)
05-01-2009 9:24 AM
Reply to: Message 1 by Percy
05-01-2009 8:57 AM


I looked up the transcripts from the Dover trial as I had a feeling this issue was addressed there.

I found a reference to this paper which gives an overview of the origination of new genetic information:

http://www3.uta.edu/faculty/betran/pdfs/naturereviews.pdf

Here's the abstract.

Nanogecko - read this and see what you think.

Rich

THE ORIGIN OF NEW GENES: GLIMPSES FROM THE YOUNG AND OLD
Manyuan Long, Esther Betrán, Kevin Thornton and Wen Wang
Genome data have revealed great variation in the numbers of genes in different organisms, which indicates that there is a fundamental process of genome evolution: the origin of new genes. However, there has been little opportunity to explore how genes with new functions originate and evolve. The study of ancient genes has highlighted the antiquity and general importance of some mechanisms of gene origination, and recent observations of young genes at early stages in their evolution have unveiled unexpected molecular and evolutionary processes.

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Percy
Member
Posts: 18492
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.8


Message 4 of 458 (507061)
05-01-2009 9:37 AM
Reply to: Message 3 by Peepul
05-01-2009 9:24 AM


Thanks much for this, I've started reading the paper but will probably have to finish later because I have to leave soon.

But I wanted to note for NanoGecko that the paper appears to be about the origin of new genes. This is very much on-topic, but just so there's no confusion I want to make clear that my example addressed the simpler case of the origin of a new allele.

--Percy


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Dr Jack
Member (Idle past 276 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 5 of 458 (507064)
05-01-2009 9:51 AM
Reply to: Message 1 by Percy
05-01-2009 8:57 AM


Whether any gene is expressed is a function of many things, the one we're most familiar with being the dominant/recessive characteristic.

Nit-picking, I'm afraid, but dominant/recessive is usually down to the intereaction of the proteins (often enzymes) produced by the two alleles not the differential expression of them.


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pandion
Member (Idle past 1172 days)
Posts: 166
From: Houston
Joined: 04-06-2009


Message 6 of 458 (507086)
05-01-2009 11:53 AM
Reply to: Message 4 by Percy
05-01-2009 9:37 AM


While Percy's definition of information as the number of bits necessary to represent the message in correct, his example of "genes" is misleading. In principle, any mutation that produces a sequence of bases that did not previously exist in a genome is an increase in information since the number of bits necessary to represent the genome has increased. Thus, if the original three sequences of 6 bases (2 codons) mutated as specified, there would be produced an additional sequence of 6 bases (2 codons) that did not exist before. Simple. It becomes obvious when you consider that to represent the bases at these 6 loci has required the writing of an additional line of information to represent the possibilities.

However (and I'm sure that Percy understands this), genes are actually composed of thousands of bases that make up thousands of codons that encode sequences that represent polymers that are thousands of amino acids long. I know that the point may seem obvious, unless you are unfamiliar with the topic. It's not all that important, I just thought it should be pointed out.

"Increase of genetic information" is just another way of saying genetic diversity. Any increase of genetic diversity is therefore, by definition, an increase in information. The specific example that Percy gave is an example of an increase in the molecular diversity of a hypothetical genome. While the example is a case of the addition of a new molecular allele, it is not a new genetic allele. You see, GGx (x being any of cytosine, adenine, guanine or uracil/thymine) always encodes the amino acid glycine, and ACx always encodes the amino acid Threonine. In other words, all 4 molecular alleles produce exactly the same sequence of amino acids in the resultant protein, and thus represent the same genetic allele. A mutation in the second G in the codon GGA would encode a different amino acid (GAA = glutamic acid, GCA = Alanine, GUA = Valine). The same principle is true for the other specified codons (GGC, ACG, ACA)

I may be picking nits here, but to someone who is unfamiliar with genetics or molecular biology then the example may be misleading. You can find the genetic code lots of places on the web, even Wikipedia.

Percy is also correct that the paper is about the origin of new genes, not the origin of new alleles.

Also, Mr. Jack is also quite correct. It is the interaction of the proteins involved that produce variations in dominance. Hypothetically, a single point mutation could cause a change that is dominant and shows up in the phenotype - which is, I think, Percy's point.

In the other thread the demand was made for one example of where natural selection added information. Percy correctly responded that it doesn't. In fact, quite the contrary is true. There are several mechanisms of evolution, some of which add genetic diversity (information in the genome) and some which remove it. Percy pointed out that natural selection (sexual selection and artificial selection as well) remove diversity. The same is true of genetic drift, biased variation, and non-random mating, other mechanisms of evolution. On the other hand, mutation, geneflow, moveable elements, and recombination add diversity.

Edited by pandion, : To add comment


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Percy
Member
Posts: 18492
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.8


Message 7 of 458 (507121)
05-01-2009 4:58 PM
Reply to: Message 6 by pandion
05-01-2009 11:53 AM


pandion writes:

I may be picking nits here...

Well, maybe, but they're good points none the less. I just put down random codons without regard to whether they coded for the same amino acid or not. If it becomes necessary I'll improve the example for NanoGecko.

--Percy


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pandion
Member (Idle past 1172 days)
Posts: 166
From: Houston
Joined: 04-06-2009


Message 8 of 458 (507124)
05-01-2009 5:23 PM


It also occurs to me that the first quote from NanoGecko is actually wrong.

NanoGecko writes:

It is just as well that the DNA contains so many base pairs of coded information, and that there is a safety mechanism in that usually both parents need to have the copying error (mutation) before the mutation will express itself in the offspring.

As pointed out later, it depends on the proteins produced. However, in one of the most famous and documented cases of evolution by natural selection, the mutation was immediately apparent. The first notice of a dark morph in the Peppered moth (Biston betularia) was in 1848. Until then all observed moths had been of the light-speckled variety. From then until 1895 the percentage of dark morphs increased until it had reached 95% in polluted areas. As pollution was reduced during the last half of the 20th century, the number of dark morphs also declined.

My point here is that the dark morph (called carbonaria) was caused by a single point mutation. The mutation and the gene has been identified. The mutated gene is dominant. Thus, heterozygous moths are dark.


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jaywill
Member (Idle past 113 days)
Posts: 4519
From: VA USA
Joined: 12-05-2005


Message 9 of 458 (507130)
05-01-2009 6:18 PM
Reply to: Message 8 by pandion
05-01-2009 5:23 PM


As pointed out later, it depends on the proteins produced. However, in one of the most famous and documented cases of evolution by natural selection, the mutation was immediately apparent. The first notice of a dark morph in the Peppered moth (Biston betularia) was in 1848. Until then all observed moths had been of the light-speckled variety. From then until 1895 the percentage of dark morphs increased until it had reached 95% in polluted areas. As pollution was reduced during the last half of the 20th century, the number of dark morphs also declined.

My point here is that the dark morph (called carbonaria) was caused by a single point mutation. The mutation and the gene has been identified. The mutated gene is dominant. Thus, heterozygous moths are dark.

Should we regard that as evidence that humans descended from ape like animals over millions of years?


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Blue Jay
Member (Idle past 869 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 10 of 458 (507133)
05-01-2009 6:24 PM
Reply to: Message 9 by jaywill
05-01-2009 6:18 PM


Hi, Jaywill.

Good to see you(r words) again.

jaywill writes:

Should we regard that as evidence that humans descended from ape like animals over millions of years?

You should regard it as evidence that humans could have evolved from ape-like animals, because all necessary steps have been shown to be possible.

You are correct that it is not direct evidence that this did happen: but, that isn't the point of this thread. Percy wants to discuss how new genetic "information" can arise through mutation.


-Bluejay (a.k.a. Mantis, Thylacosmilus)

Darwin loves you.


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pandion
Member (Idle past 1172 days)
Posts: 166
From: Houston
Joined: 04-06-2009


Message 11 of 458 (507136)
05-01-2009 7:03 PM
Reply to: Message 9 by jaywill
05-01-2009 6:18 PM


jaywill writes:

Should we regard that as evidence that humans descended from ape like animals over millions of years?

Why on earth would you even ask such a question? Why do you feel that moths should be involved in the evolution of humans? All living organisms are the result of evolution. They are all descended from previous organisms that were different.

I can present some evidence that humans share a common ancestor with the other apes. Would you like to learn about it?

Edited by pandion, : To correct phrasing.

Edited by pandion, : No reason given.


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OriginLifeandDeath
Junior Member (Idle past 3597 days)
Posts: 9
Joined: 05-14-2009


Message 12 of 458 (508572)
05-14-2009 9:30 PM
Reply to: Message 11 by pandion
05-01-2009 7:03 PM


http://www.cafepress.com/Origin_of_Death

A mosaic book which examines the causes of life and death by cobbling various scientific investigations into an unmistakable conclusion: Charles Darwin and creationist prove to be both right and the same.
Synopsis
Life on our planet has adapted to live in the Antarctic, thermal fissures, sulfur pools, near molten lava (extremophiles), fresh and salt water, as well as Florida and other more comfortable environs. Given that life is so virile and adaptive, why does it succumb to death just because it has lived? By embracing Darwin's work, studying it and determining its limits of application, we are left with a firm understanding of evolution (origin of species). The fit is great and supported by a wealth of evidence. Darwin's theory propels a very accurate understanding of the origin of species but not the origin of life and death. Evolution provides no answers or scientific explanation for the origin of life and death. This is not because Darwin's work is unfinished but rather because evolution has no application here. One of the main arguments employed by creationists against the theory of evolution is expressed in the form of a rhetorical question, how can chance mutations (mistakes) create all the complicated life forms we see? It is a good question. The question's underlying assumption maintains that evolutionists believe that organisms, which more recently evolved, are further evolved, improved and therefore more complex than earlier creatures on the evolutionary path. Indeed, most evolutionists believe this hierarchy of complexity. But what if that very first cell was in fact more complicated than all life that followed? The answer to this question places evolution and creationism on the same track. This book reveals their co-existence with an enormity of sceintific fact. This book reveals that evolution is God's creation to serve the life he also created. Darwin actually does more to prove the existence of a creator than anyone.

The content is a new topic here

Edited by Adminnemooseus, : Hid content and added banner.

Edited by Adminnemooseus, : Add link to new topic.


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Coyote
Member (Idle past 278 days)
Posts: 6117
Joined: 01-12-2008


Message 13 of 458 (508583)
05-14-2009 10:04 PM
Reply to: Message 12 by OriginLifeandDeath
05-14-2009 9:30 PM


Flogging your book?
This is the second place I've seen where you've posted the same reference to a self-published book.

Are you flogging your own book by any chance? Sales slow?

Edited by Adminnemooseus, : Hid content, added banner.


Religious belief does not constitute scientific evidence, nor does it convey scientific knowledge.
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slevesque
Member (Idle past 2812 days)
Posts: 1456
Joined: 05-14-2009


Message 14 of 458 (508886)
05-17-2009 2:51 AM
Reply to: Message 8 by pandion
05-01-2009 5:23 PM


As pointed out later, it depends on the proteins produced. However, in one of the most famous and documented cases of evolution by natural selection, the mutation was immediately apparent. The first notice of a dark morph in the Peppered moth (Biston betularia) was in 1848. Until then all observed moths had been of the light-speckled variety. From then until 1895 the percentage of dark morphs increased until it had reached 95% in polluted areas. As pollution was reduced during the last half of the 20th century, the number of dark morphs also declined.

I believe that evolutionary biologist L. Harrison Matthews wrote that the peppered moth case was simple natural selection, but not evolution in action. Am I missing something here ?

"The [peppered moth] experiments beautifully demonstrate natural selection—or survival of the fittest—in action, but they do not show evolution in progress; for however the populations may alter in their content of light, intermediate or dark forms, all the moths remain, from beginning to end, Biston betularia."

—*L. Harrison Matthews, "Introduction," to Charles Darwin's Origin of the Species (1971 edition), p. xi


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slevesque
Member (Idle past 2812 days)
Posts: 1456
Joined: 05-14-2009


Message 15 of 458 (508887)
05-17-2009 2:52 AM


By the way, has anyone here read John Sanford's book ''genetic entropy ...'' ?
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