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Author Topic:   Evolving New Information
Percy
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Posts: 19073
From: New Hampshire
Joined: 12-23-2000
Member Rating: 3.3


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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Percy
Member
Posts: 19073
From: New Hampshire
Joined: 12-23-2000
Member Rating: 3.3


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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Percy
Member
Posts: 19073
From: New Hampshire
Joined: 12-23-2000
Member Rating: 3.3


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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Percy
Member
Posts: 19073
From: New Hampshire
Joined: 12-23-2000
Member Rating: 3.3


Message 16 of 458 (508923)
05-17-2009 8:47 AM
Reply to: Message 14 by slevesque
05-17-2009 2:51 AM


slevesque writes:

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?

Evolution is descent with modification and natural selection, but Harrison is correct that it is primarily natural selection at work in the case of the peppered moth studies. But the passage you cite from him says that it isn't evolution because the peppered moth did not evolve into a new species, and that's incorrect.

Evolution proceeds in tiny steps. A change from one species to the next occurs through the accumulation of many tiny evolutionary steps, of descent with modification followed by natural selection over and over and over again through the generations. Each generation is one step. Saying that the small amount of change observed in the peppered moth studies was not evolution is like saying that you're not really going for a walk unless you walk all the way to the next city.

Just as you can go for a short walk and change your location a little, or you can go for long walks and change your location a lot, we can watch evolution for a short while and observe a little change, or we can watch evolution for a long while and observe a lot of change. But there's a problem watching evolution for a long while. Except for organisms with very short lifetimes like bacteria or even mosquitoes to an extent, the number of generations any scientific study can observe is very small.

The slow pace of evolution is paralleled by the slow pace of the erosion of mountains. We know that mountains typically erode by a few inches per year, but we're never going to observe mountains eroding all the way down to plains because it takes millions of years. We just have to rely upon the fact that once a mountain erodes a few inches this year, there's nothing to prevent it from eroding a few more inches next year, and the year after, and the year after that, and so on for eternity.

Each generation brings about a tiny amount of evolutionary change because reproduction is imperfect. Every generation contains new mutations not previously present in the population. Natural selection operates on these differences, and individuals with the more favorable changes contribute disproportionately to the genes of the next generation. And there's nothing to prevent this from happening in the next generation, and the one after that, and the after that, and so on for eternity. Changes can accumulate to the point where a species actually becomes a different species, and this is especially true when there are changing environmental conditions which increases selection pressures.

--Percy


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Percy
Member
Posts: 19073
From: New Hampshire
Joined: 12-23-2000
Member Rating: 3.3


Message 27 of 458 (509157)
05-19-2009 3:09 AM
Reply to: Message 25 by slevesque
05-19-2009 2:16 AM


Have you read the book The Beek of the Pinch? :D

--Percy


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Percy
Member
Posts: 19073
From: New Hampshire
Joined: 12-23-2000
Member Rating: 3.3


Message 33 of 458 (509189)
05-19-2009 8:35 AM
Reply to: Message 30 by Huntard
05-19-2009 3:37 AM


end e mispeled bek to.

--perch


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Percy
Member
Posts: 19073
From: New Hampshire
Joined: 12-23-2000
Member Rating: 3.3


Message 40 of 458 (509491)
05-22-2009 7:12 AM
Reply to: Message 38 by slevesque
05-22-2009 1:27 AM


slevesque writes:

But if, after having shown me this, you tell me that such a mechanism, extrapolated to vast amounts of time, could turn a finch into let's say, a horse, then I will not agree with you.

Neither would I, any one familiar with biology or an experts in the field. So you are in good company. :)

Ok so why do I have these as examples of evolution in my biology book then?

So your biology book provides the example of finches evolving into horses? Interesting. I suggest you use it for heating purposes the next cold winter.

I mean, they talk for about 10-15 pages about the happening of life in ancient-earth oceans, then about how bacterias evolved into fish, to ampibians, etc. from dinosaurs to birds, from australopithecus to humans, etc.

Now this is entirely reasonable, so maybe you shouldn't burn your biology book after all. A finch evolving into a horse is not the same as what you say here. Birds aren't even mammals.

a good read would be Genetic Entropy & the Mystery of the Genome by Dr. John Sanford...I can tell you his book is one of the must bullet-proof I have seen on both sides. (and I read quite a lot)

Thanks for the assurances, but you just revealed that you think a finch evolving into a horse is a valid example of evolution, so the evidence would suggest that despite your voluminous reading you lack the understanding of biology necessary for assessing the validity of what you read. About Sanford Wikipedia says:

Wikipedia writes:

An advocate of intelligent design, in 2005 Sanford testified in the Kansas evolution hearings on behalf of intelligent design, during which he denied the principle of common descent and "humbly offered ... that we were created by a special creation, by God." He also stated that he believed the age of the Earth was "Between 5,000 and 100,000" years.

By the way, note Sanford's somewhat conflicting views, where he accepts ID while simultaneously rejecting common descent and believing in a young Earth just like young Earth creationists. Michael Behe, arguably the founder of the ID movement, accepts common descent and rejects a young Earth. Could I suggest to you that Sanford is not a reliable source, and that the fact that a read of his book doesn't reveal this to you further suggests that you be cautious in trusting your intuitions about biology.

--Percy


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Percy
Member
Posts: 19073
From: New Hampshire
Joined: 12-23-2000
Member Rating: 3.3


Message 45 of 458 (509541)
05-22-2009 10:05 AM
Reply to: Message 42 by LucyTheApe
05-22-2009 9:45 AM


Re: gca
I think you're completely lost. I presented a simple example illustrating how random mutations can increase information. Your complaint makes no more sense than if I were explaining algebra and after I presented the problem "y=4x+7" you complained that I had no way of knowing the relationship between x and y.

But there's more than one way to explain anything, so if the correspondence to actual eye color bothers you then we'll just simplify the example.

Imagine that in a population, one of the genes has three messages that it can communicate. Each message consists of a sequence of six nucleotides (the nucleotides for DNA are guanine, adenine, cytosine and thymine, and they're represented by the letters G, A, C and T):

  • GGAACG
  • GGAACA
  • GGCACG

Since there are three messages in the message set for this gene, the amount of information it can communicate is log23 = 1.585 bits.

Now imagine that in the next generation one of the offspring experiences a mutation in this gene. Had there been no mutation then it would have received the GGCACG message, but the mutation switches the last nucleotide from guanine to adenine, and the message becomes GGCACA. Now in the genome for the population there exists four messages for this gene:

  • GGAACG
  • GGAACA
  • GGCACG
  • GGCACA

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.

--Percy

Edited by Percy, : Typo.

Edited by Percy, : Still learning to type, apparently. Anyone finding more typos, please be specific.


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Percy
Member
Posts: 19073
From: New Hampshire
Joined: 12-23-2000
Member Rating: 3.3


Message 65 of 458 (509651)
05-23-2009 6:10 AM
Reply to: Message 57 by slevesque
05-23-2009 3:22 AM


slevesque writes:

Technically, what prevents mutations+natural selection to have birds become mammals in the theory of evolution? Nothing of course. I wan't saying it happened in the past, I was saying that according to evolution, it could happen in the future.

This is how you began your exchange with Onifre in Message 25

slevesque in Message 25 writes:

But if, after having shown me this, you tell me that such a mechanism, extrapolated to vast amounts of time, could turn a finch into let's say, a horse, then I will not agree with you.

You put the words in Onifre's mouth ("You tell me that..."), but no one here would ever suggest the possibility of an existing species evolving across "vast amounts of time" into a different existing species. While technically not impossible in that it doesn't violate any known physical laws, it is both incredibly unlikely and in this thread incredibly irrelevant.

What would be more relevant is if you addressed your contradictory advocacy of a young earth in this thread and an old earth in the Misconceptions in Relativity thread.

--Percy


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Percy
Member
Posts: 19073
From: New Hampshire
Joined: 12-23-2000
Member Rating: 3.3


Message 74 of 458 (509732)
05-24-2009 8:54 AM
Reply to: Message 67 by slevesque
05-24-2009 1:36 AM


slevesque writes:

And you'll have to tell me how I advocated an old earth on the cosmology thread, since I do remember only saying that Carmeli was advocating an old earth, not me.

Your inability to express a consistent viewpoint indicates inner confusion. Are you saying that you reject an ancient Earth and accept Carmeli's cosmological views that advocate the ancient Earth that you reject? Are you saying that preserved dinosaur protein indicates the Earth is young, or that dinosaurs actually survived until a few thousand years ago?

--Percy


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Percy
Member
Posts: 19073
From: New Hampshire
Joined: 12-23-2000
Member Rating: 3.3


Message 77 of 458 (510077)
05-27-2009 8:09 AM
Reply to: Message 75 by Dr Adequate
05-24-2009 10:16 AM


Dr Adequate writes:

That would be Kimura the founder of neutralism and the author of The Neutral Theory of Molecular Evolution, yes? Can you quote him as saying that there are no neutral mutations?

Until I read an article in this month's Scientific American (How Trivial DNA Changes Can Hurt Health) I would have replied in the same way, but now I'm not so sure. Maybe there really is no such thing as a neutral mutation.

The example in the SciAm article was of a neutral mutation that still produces the identical protein. Let's say that in the gene for a certain protein that one codon mutates from GGA to GGG, which still produces glycine. The RNA machinery will still produce the same protein, but it turns out that because the particular chemical that RNA uses to interpret GGA properly is much more common than for interpreting GGG, the mutation to GGG causes the protein to be produced less efficiently or with greater error. As expressed at one point in the article:

It turned out that tRNAs corresponding to those synonymous codons typically are not equally abundant within the cell. Most important, then, a gene that contains more of the codons matching the relatively abundant tRNAs would be translated faster, because the higher concentration of those tRNAs would make them more likely to be present when needed.

Given the possibility of such subtle effects as the concentration levels of very specific chemicals within the cell upon the protein factory, completely neutral mutations now seem much less likely to me.

A news brief in the same issue (Genetic Copy Variations and Disease) described how high level mutations called copy number mutations are far more common than originally suspected:

In 2004, however, things changed. Two groups of researchers published the first genome-wide CNV maps, which illustrated that variation in gene quantity is actually quite common: each group found about 12 copy number imbalances per person.

...

Scherer and his colleagues, who included population geneticist Matthew Hurles of the Wellcome Trust Sanger Institute in Cambridge, England, followed up with a higher-resolution CNV study in 2006, which analyzed DNA from 270 individuals and identified an average of 47 copy number variations per person. And in 2007 researchers sequenced the genome of genetic pioneer J. Craig Venter and found 62 copy number variations. Evidently, Hurles says, “it’s not normal to be walking around with the perfect genome.”

So not only are neutral mutations less neutral than we thought, the amount of genetic variation in members of the same species may be systematically underestimated. In other words, there's more new information evolving all the time than we may have previously thought.

--Percy

Edited by Percy, : Add missing close parenthesis.


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Percy
Member
Posts: 19073
From: New Hampshire
Joined: 12-23-2000
Member Rating: 3.3


Message 81 of 458 (510253)
05-29-2009 9:47 AM
Reply to: Message 80 by LucyTheApe
05-29-2009 9:09 AM


Re: Why not?
LucyTheApe writes:

Because according to Percy's view there are 4096 different kinds of eyes (color). Now add information to this!

No, according to *you* there are 4096 different kinds of eye color. 4096 is the maximum possible number of unique messages that can created with a six character sequence of four characters. I said there were three messages in the message set:

  • GGAACG
  • GGAACA
  • GGCACG

What this means is that each organism in our population has only one of these three sequences for this gene. Some organisms have the CGAACG sequence for this gene, some have GGAACA, and some have GGCACG. No other sequence exists for this gene anywhere in this population, which means that when communicating information about this gene to offspring during reproduction, only one of those three messages can be communicated, unless...

Unless there's an error while the sequence is being communicated. In other words, if there's an error during reproduction (a mutation), then the message for this gene may be communicated incorrectly. In my example I said that the GGCACG sequence experienced an error during reproduction and became GGCACA. Now, in addition to the three sequences that the population originally had, there is one organism that has the new sequence GGCACA, and so the number of possible sequences for this gene in our population is now four:

  • GGAACG
  • GGAACA
  • GGCACG
  • GGCACA

When there were only three messages in the message set for this gene, the amount of information it could communicate was log23 = 1.585 bits. 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.

--Percy

Edited by Percy, : Grammar.

Edited by Percy, : Grammar.


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Percy
Member
Posts: 19073
From: New Hampshire
Joined: 12-23-2000
Member Rating: 3.3


Message 92 of 458 (510341)
05-30-2009 6:49 AM
Reply to: Message 89 by slevesque
05-30-2009 4:36 AM


From Message 83:

slevesque in Message 83 in reply to Dr Adequate writes:

The interpretation creationist do of it is debatable, but for that you'll have to read the book instead of just reading the critics on amazone.com ;)

From Message 89:

slevesque in Message 89 in reply to Dr Adequate writes:

I think it is gonna be very difficult to discuss this with your aggressive behavior coupled with the fact that you haven't read the book.

If someone actually reads the book that will be a nice bonus for you, but don't expect it to happen. The Forum Guidelines require that you make your arguments in your own words:

  1. Bare links with no supporting discussion should be avoided. Make the argument in your own words and use links as supporting references.

You're referencing a book instead of a link, but the same principle applies. Make the argument in your own words. The purpose of debate is so you can assess how effectively *you* can construct and support an argument, not someone else.

About the funny characters, were you trying to say ƒ(μ) or something like that?

--Percy


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Percy
Member
Posts: 19073
From: New Hampshire
Joined: 12-23-2000
Member Rating: 3.3


Message 107 of 458 (511109)
06-06-2009 7:41 AM
Reply to: Message 106 by slevesque
06-06-2009 2:23 AM


See Message 3.

--Percy


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Percy
Member
Posts: 19073
From: New Hampshire
Joined: 12-23-2000
Member Rating: 3.3


Message 110 of 458 (512497)
06-18-2009 2:32 PM
Reply to: Message 109 by AustinG
06-18-2009 1:40 PM


Re: Joining in
Message 1 defines information in the context of mutations.

--Percy


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