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Author Topic:   Evolving New Information
Taq
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Posts: 8101
Joined: 03-06-2009
Member Rating: 4.2


Message 76 of 458 (510013)
05-26-2009 6:37 PM
Reply to: Message 58 by slevesque
05-23-2009 3:52 AM


slevesque writes:

Man and chimp differ by at least 150 million nucleotides, representing at least 40 million hypothetical mutations. So if man evolved from a chimp-like creature, then during that process there were at least 20 million mutations fixed within the human lineage (the other 20 million being in the chimp lineage). This means you have to fix over 3 mutations per year in the population (considering the divergence 6 millions years ago). Even considering generations of 1 year, this is, at best, unrealistic. (human generations are currently 20 years)

Haldane had calculated in 1957, that it takes, on average, 300 generations to select a single mutation to fixation in a population. Although I agree there has been revisions of his calculations in the past fifty years, there are no actual numbers that come even close to the fixation rates needed. All the fixations not done by selection have to be done by genetic drift, which is way slower then selection.

Not all mutations are point mutations. You must also factor in indels. If a 100 base indel becomes fixed you are fixing 100 bases all at the same time.

So to answer your question, even if we assume that mutations can create the different information between chimps and humans, even the evolutionnary time scale is not long enough to allow for such massive changes, unless you assume impossible fixation rates.

As others have shown, the mutation rate needed to produce the differences seen between humans and chimps is pretty close to the mutation rate observed in humans as others have pointed out.


This message is a reply to:
 Message 58 by slevesque, posted 05-23-2009 3:52 AM slevesque has responded

Replies to this message:
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Percy
Member
Posts: 18879
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


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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Replies to this message:
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LucyTheApe
Inactive Member


Message 78 of 458 (510233)
05-29-2009 7:10 AM
Reply to: Message 1 by Percy
05-01-2009 8:57 AM


Percy writes:

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.

I'll take issue with it Percy.

There are 6 lots of 4 possibilities according to your model. That's 46 different possibilities. You can't add information to that but it's interesting to hear you talk about messages.

Edited by LucyTheApe, : gammar


There no doubt exist natural laws, but once this fine reason of ours was corrupted, it corrupted everything.

blɛz paskal


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Replies to this message:
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NosyNed
Member
Posts: 8863
From: Canada
Joined: 04-04-2003
Member Rating: 5.3


Message 79 of 458 (510240)
05-29-2009 8:31 AM
Reply to: Message 78 by LucyTheApe
05-29-2009 7:10 AM


Why not?
There are 6 lots of 4 possibilities according to your model. That's 46 different possibilities. You can't add information to that but it's interesting to hear you talk about messages.

Why not?


This message is a reply to:
 Message 78 by LucyTheApe, posted 05-29-2009 7:10 AM LucyTheApe has responded

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LucyTheApe
Inactive Member


Message 80 of 458 (510244)
05-29-2009 9:09 AM
Reply to: Message 79 by NosyNed
05-29-2009 8:31 AM


Re: Why not?
NosyNed writes:

Why not?

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


There no doubt exist natural laws, but once this fine reason of ours was corrupted, it corrupted everything.

blɛz paskal


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Percy
Member
Posts: 18879
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


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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Huntard
Member (Idle past 586 days)
Posts: 2870
From: Limburg, The Netherlands
Joined: 09-02-2008


Message 82 of 458 (510255)
05-29-2009 10:15 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 there aren't. There are only 3 in the beginning, and four after the mutation. Seriously, what is so hard to understand here?

Edited by Huntard, : Spellings


I hunt for the truth

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 Message 80 by LucyTheApe, posted 05-29-2009 9:09 AM LucyTheApe has not yet responded

    
slevesque
Member (Idle past 2931 days)
Posts: 1456
Joined: 05-14-2009


Message 83 of 458 (510329)
05-30-2009 3:15 AM
Reply to: Message 75 by Dr Adequate
05-24-2009 10:16 AM


Now I'll try to make things clearer on here.

Find Kimura's mutation distribution graphic, you will see that 0 (neutrality) is an asymptote.

Also on Muller ratchet, notice that it was never observed to cause the extinction of bacteria species. It was, in fact, very, very, very seldom observed. Remember that at the time Muller thought of this, technology wasn't good enough for him to test it. It is still much more hypothetical than experimental, exactly because of what I was saying earlier.

The only experimental documentation of muller's ratchet I found is this:
- Chao, 1990, Fitness of an RNA virus decreased by Muller's ratchet, Nature 348: 454 - 455

Muller ratchet has not yet been falsified. The vast majority of geneticist agree that it exists. You question why we do not see it causing the extinction of bacterias ? It is because of what I have explained (noise, etc.). Ask a geneticist and he will give you aproximately the same answer. Its existence in bacteria populations is not questioned by evolutionist or creationist.

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 ;)


This message is a reply to:
 Message 75 by Dr Adequate, posted 05-24-2009 10:16 AM Dr Adequate has responded

Replies to this message:
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slevesque
Member (Idle past 2931 days)
Posts: 1456
Joined: 05-14-2009


Message 84 of 458 (510330)
05-30-2009 3:24 AM
Reply to: Message 76 by Taq
05-26-2009 6:37 PM


I agree some mutations account to multiple variations in nucleotides. But the ''representing at least 40 million mutations fixed'' include all types of mutations.

This message is a reply to:
 Message 76 by Taq, posted 05-26-2009 6:37 PM Taq has not yet responded

  
slevesque
Member (Idle past 2931 days)
Posts: 1456
Joined: 05-14-2009


Message 85 of 458 (510332)
05-30-2009 3:45 AM
Reply to: Message 62 by Dr Adequate
05-23-2009 4:54 AM


Ok, I'll try to follow you here.

According to your calculations, how many mutations would be fixed in a single generation ? Your equation is gMs if I'm not mistaken.

Now 1 generation means g=1. M=1.7 ~ 10^-8 and s=3 000 000 000

So, according to you, there is 510 mutations fixed per generation, am I correct on this ?

If so, why the part on ƒÊ ?


This message is a reply to:
 Message 62 by Dr Adequate, posted 05-23-2009 4:54 AM Dr Adequate has responded

Replies to this message:
 Message 87 by Dr Adequate, posted 05-30-2009 4:21 AM slevesque has responded

  
Dr Adequate
Member
Posts: 16107
Joined: 07-20-2006
Member Rating: 7.7


Message 86 of 458 (510334)
05-30-2009 4:06 AM
Reply to: Message 83 by slevesque
05-30-2009 3:15 AM


Find Kimura's mutation distribution graphic, you will see that 0 (neutrality) is an asymptote.

I'm not sure what you think that means, but I'm fairly sure that you're wrong. What do you mean by "Kimura's mutation distribution graphic"? Is it one of the figures in The Neutral Theory Of Molecular Evolution (yes, that's The Neutral Theory Of Molecular Evolution) and if so, which one? If you will tell me which figure, I shall tell you what it means.

And I am absolutely certain that Kimura, the founder of neutralism, did not deny the existence of neutral mutations.

Also on Muller ratchet, notice that it was never observed to cause the extinction of bacteria species. It was, in fact, very, very, very seldom observed. Remember that at the time Muller thought of this, technology wasn't good enough for him to test it. It is still much more hypothetical than experimental, exactly because of what I was saying earlier.

The only experimental documentation of muller's ratchet I found is this:
- Chao, 1990, Fitness of an RNA virus decreased by Muller's ratchet, Nature 348: 454 - 455

Muller ratchet has not yet been falsified. The vast majority of geneticist agree that it exists. ... Its existence in bacteria populations is not questioned by evolutionist or creationist.

Again, I don't see what you're driving at. I said that the concept of Muller's ratchet only applies to asexually reproducing organisms, such as bacteria, in which I am, of course, right.

Your reply that its existence in bacteria is not questioned does not constitute a rebuttal. I am not questioning its existence in bacteria. I am asserting its existence in bacteria.

It is because of what I have explained (noise, etc.).

Your excuse about there being no "noise" in bacteria, besides being palpable rubbish, was intended as an excuse to allow you to pretend that bacteria are immune from accumulating deleterious mutations, remember? If you are now admitting that bacteria are subject to Muller's ratchet, then you admit that they do in fact do so, and that moreover they do so by a mechanism that does not apply to sexually reproducing organisms.

Ask a geneticist and he will give you aproximately the same answer.

No.

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

As he can't explain what he's talking about, and you are at least willing to try, I believe I'll stick to debating with you.


This message is a reply to:
 Message 83 by slevesque, posted 05-30-2009 3:15 AM slevesque has responded

Replies to this message:
 Message 89 by slevesque, posted 05-30-2009 4:36 AM Dr Adequate has responded

  
Dr Adequate
Member
Posts: 16107
Joined: 07-20-2006
Member Rating: 7.7


Message 87 of 458 (510335)
05-30-2009 4:21 AM
Reply to: Message 85 by slevesque
05-30-2009 3:45 AM


Ok, I'll try to follow you here.

According to your calculations, how many mutations would be fixed in a single generation ? Your equation is gMs if I'm not mistaken.

Now 1 generation means g=1. M=1.7 ~ 10^-8 and s=3 000 000 000

So, according to you, there is 510 mutations fixed per generation, am I correct on this ?

I make it 51.

If so, why the part on ƒÊ ?

I don't know how the characters in red display on your browser, but on mine they're the fortissimo symbol followed by a capital E with a circumflex. This makes your question someone opaque.


This message is a reply to:
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Replies to this message:
 Message 88 by slevesque, posted 05-30-2009 4:29 AM Dr Adequate has responded

  
slevesque
Member (Idle past 2931 days)
Posts: 1456
Joined: 05-14-2009


Message 88 of 458 (510337)
05-30-2009 4:29 AM
Reply to: Message 87 by Dr Adequate
05-30-2009 4:21 AM


I recalculated and got 51 also

that last character didn't come out well, it was supposed to be the u


This message is a reply to:
 Message 87 by Dr Adequate, posted 05-30-2009 4:21 AM Dr Adequate has responded

Replies to this message:
 Message 90 by Dr Adequate, posted 05-30-2009 4:38 AM slevesque has responded

  
slevesque
Member (Idle past 2931 days)
Posts: 1456
Joined: 05-14-2009


Message 89 of 458 (510338)
05-30-2009 4:36 AM
Reply to: Message 86 by Dr Adequate
05-30-2009 4:06 AM


I thought you were asking why muller's ratchet didn't provoke the extinction of bacterias ?

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.

Dr. Sanford doesn't simply apply Muller's ratchet on sexual species, he ellaborates the concept of mutation accumulations to sexual species. This is very different. It is like an extension of Muller's ratchet, if you like.


This message is a reply to:
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Replies to this message:
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Dr Adequate
Member
Posts: 16107
Joined: 07-20-2006
Member Rating: 7.7


Message 90 of 458 (510339)
05-30-2009 4:38 AM
Reply to: Message 88 by slevesque
05-30-2009 4:29 AM


I'm fairly sure I didn't say "fu" anywhere ... which shows great restraint on my part (joke).

If you now get 51 fixations per generation, does that mean that you now understand what's going on? If not, where does "fu" come into it? Can you quote?


This message is a reply to:
 Message 88 by slevesque, posted 05-30-2009 4:29 AM slevesque has responded

Replies to this message:
 Message 93 by slevesque, posted 05-31-2009 2:52 AM Dr Adequate has responded

  
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