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Author Topic:   Information Changes in DNA by logical Analysis
Dr Adequate
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Posts: 16097
Joined: 07-20-2006


Message 16 of 80 (531441)
10-17-2009 11:34 PM
Reply to: Message 15 by Percy
10-17-2009 9:01 PM


But here you and WK are talking about information in a gene pool. I'm talking about information in a genome.
This message is a reply to:
 Message 15 by Percy, posted 10-17-2009 9:01 PM Percy has responded

Replies to this message:
 Message 17 by Percy, posted 10-18-2009 7:22 AM Dr Adequate has responded

  
Percy
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Posts: 18498
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.9


Message 17 of 80 (531480)
10-18-2009 7:22 AM
Reply to: Message 16 by Dr Adequate
10-17-2009 11:34 PM


If you're only considering the genes of a single individual then reproduction cannot be part of the conversation, so you must be looking at DNAs role in controlling the cell machinery. Do I have that right?

--Percy


This message is a reply to:
 Message 16 by Dr Adequate, posted 10-17-2009 11:34 PM Dr Adequate has responded

Replies to this message:
 Message 19 by Dr Adequate, posted 10-19-2009 6:59 AM Percy has responded

    
Wounded King
Member (Idle past 2268 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 18 of 80 (531623)
10-19-2009 6:14 AM
Reply to: Message 12 by Dr Adequate
10-17-2009 12:34 AM


It is hardly news that creationist/Iders use logically flawed arguments. I'm just pointing out that these are the arguments they use.

I found your explanation here very closely follows a critique in a paper I was reading where they discuss Muller's ratchet (Mustonnen and Lassig, 2009).

Mustonnen and Lassig writes:

It is instructive to contrast this view of adaptive evolution with Muller's ratchet, a classical model of evolution by deleterious substitutions [citations removed] . This model postulates a well-adapted initial state of the genome so that all, or the vast majority of, mutations have negative fitness effects. Continuous fixations of slightly deleterious changes then lead to a stationary decline in fitness (i.e. to negative values of Φ). Similarly to the infinite-sites approximation, this model neglects compensatory mutations. In a picture of a finite number of sites, it becomes clear that every deleterious substitution leads to the opportunity for at least one compensatory beneficial mutation (or more, if the locus contributes to a quantitative trait), so that the rate of beneficial substitutions increases with decreasing fitness.

...

Thus, we reach a conclusion contrary to Muller's ratchet. Because selection in biological systems is generically time-dependent, decline of fitness is less likely even as a transient state than suggested by Muller's ratchet: the model offers no explanation of how a well-adapted initial state without opportunities of beneficial mutations is reached in the first place.

And we all know how much the ID camp love Muller's ratchet.

TTFN,

WK


This message is a reply to:
 Message 12 by Dr Adequate, posted 10-17-2009 12:34 AM Dr Adequate has responded

Replies to this message:
 Message 20 by Dr Adequate, posted 10-19-2009 7:05 AM Wounded King has not yet responded

    
Dr Adequate
Member
Posts: 16097
Joined: 07-20-2006


Message 19 of 80 (531630)
10-19-2009 6:59 AM
Reply to: Message 17 by Percy
10-18-2009 7:22 AM


If you're only considering the genes of a single individual then reproduction cannot be part of the conversation, so you must be looking at DNAs role in controlling the cell machinery. Do I have that right?

No, no, not at all. I'm talking about germ-line mutations. What I'm analyzing is the question of "information" (whatever that is) increasing or decreasing if we follow a single line of descent. We go from the genome of one individual ... to the genome of the next descendant ... to the genome of the next descendant ... and so forth.

My point there was that I'm looking at the genomes of individuals along a line of descent, I'm not considering the amount of information in a gene pool.

Edited by Dr Adequate, : No reason given.


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 Message 17 by Percy, posted 10-18-2009 7:22 AM Percy has responded

Replies to this message:
 Message 21 by Percy, posted 10-19-2009 9:25 AM Dr Adequate has not yet responded

  
Dr Adequate
Member
Posts: 16097
Joined: 07-20-2006


Message 20 of 80 (531633)
10-19-2009 7:05 AM
Reply to: Message 18 by Wounded King
10-19-2009 6:14 AM


It is hardly news that creationist/Iders use logically flawed arguments. I'm just pointing out that these are the arguments they use.

And I'm just pointing out why they're wrong. If you're going to say: "Creationists would put up such-and-such an argument", then I am going to reply by saying why that argument is deeply flawed.


This message is a reply to:
 Message 18 by Wounded King, posted 10-19-2009 6:14 AM Wounded King has not yet responded

  
Percy
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Posts: 18498
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.9


Message 21 of 80 (531655)
10-19-2009 9:25 AM
Reply to: Message 19 by Dr Adequate
10-19-2009 6:59 AM


Dr Adequate writes:

What I'm analyzing is the question of "information" (whatever that is) increasing or decreasing...

If you want to know whether information is increasing or decreasing then you need to be able to quantify it. What I haven't been able to figure out yet is how you're quantifying information.

--Percy


This message is a reply to:
 Message 19 by Dr Adequate, posted 10-19-2009 6:59 AM Dr Adequate has not yet responded

Replies to this message:
 Message 22 by NosyNed, posted 10-19-2009 9:29 AM Percy has responded
 Message 46 by JonF, posted 10-19-2009 1:40 PM Percy has responded

    
NosyNed
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Posts: 8842
From: Canada
Joined: 04-04-2003


Message 22 of 80 (531656)
10-19-2009 9:29 AM
Reply to: Message 21 by Percy
10-19-2009 9:25 AM


Quantification
If you want to know whether information is increasing or decreasing then you need to be able to quantify it. What I haven't been able to figure out yet is how you're quantifying information.

It appears this argument doesn't require a definition of the quantity just as it doesn't require a definition of what is meant by "information". It is more abstract than that -- and simpler.


This message is a reply to:
 Message 21 by Percy, posted 10-19-2009 9:25 AM Percy has responded

Replies to this message:
 Message 23 by Percy, posted 10-19-2009 9:45 AM NosyNed has not yet responded

  
Percy
Member
Posts: 18498
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.9


Message 23 of 80 (531662)
10-19-2009 9:45 AM
Reply to: Message 22 by NosyNed
10-19-2009 9:29 AM


Re: Quantification
I guess I don't understand the argument Dr Adequate is making. The OP refers to an article at SkepticWiki, but the provided link is to the main page. Is this the relevant article:

http://skepticwiki.org/index.php/Mutations_and_Information

Anyway, I began rereading this thread from scratch trying to make sure I understood it at each step along the way, and then I came to Dr Adequate's Message 4 where he refers to λ:

Dr Adequate writes:

Well, I think everyone would have to admit that λ contains no information by any sensible metric; which is why I introduced it into the argument.

So once someone explains what λ is I'll continue rereading the thread.

But in the meantime, I notice that in the SkepticWiki article it says:

SkepticWiki writes:

The most obvious problem with this argument is that the creationists who use it never say how information is to be measured in this context.

I'm seeing the same problem in this thread.

--Percy


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Replies to this message:
 Message 24 by Wounded King, posted 10-19-2009 9:47 AM Percy has acknowledged this reply
 Message 25 by Modulous, posted 10-19-2009 9:48 AM Percy has acknowledged this reply
 Message 26 by PaulK, posted 10-19-2009 9:54 AM Percy has responded
 Message 31 by Dr Adequate, posted 10-19-2009 11:33 AM Percy has responded

    
Wounded King
Member (Idle past 2268 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 24 of 80 (531663)
10-19-2009 9:47 AM
Reply to: Message 23 by Percy
10-19-2009 9:45 AM


Re: Quantification
I believe λ is Dr. A's null string which contains no DNA.

TTFN,

WK


This message is a reply to:
 Message 23 by Percy, posted 10-19-2009 9:45 AM Percy has acknowledged this reply

    
Modulous
Member (Idle past 277 days)
Posts: 7789
From: Manchester, UK
Joined: 05-01-2005


(1)
Message 25 of 80 (531664)
10-19-2009 9:48 AM
Reply to: Message 23 by Percy
10-19-2009 9:45 AM


Re: Quantification
So once someone explains what is I'll continue rereading the thread.

It's a null string - containing no letters.


This message is a reply to:
 Message 23 by Percy, posted 10-19-2009 9:45 AM Percy has acknowledged this reply

  
PaulK
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Posts: 15085
Joined: 01-10-2003
Member Rating: 3.3


Message 26 of 80 (531665)
10-19-2009 9:54 AM
Reply to: Message 23 by Percy
10-19-2009 9:45 AM


Re: Quantification
quote:

I'm seeing the same problem in this thread.

I think you are missing the point. The point of the argument is to show that even without a defined measure, given a few sensible axioms it must be possible for mutations to increase information. Relying on a specific measure would be self-defeating.


This message is a reply to:
 Message 23 by Percy, posted 10-19-2009 9:45 AM Percy has responded

Replies to this message:
 Message 27 by Percy, posted 10-19-2009 10:17 AM PaulK has responded

    
Percy
Member
Posts: 18498
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.9


Message 27 of 80 (531668)
10-19-2009 10:17 AM
Reply to: Message 26 by PaulK
10-19-2009 9:54 AM


Re: Quantification
I'm having trouble trying to put what Dr Adequate is saying into a context I'm familiar with. For example, when he says this in the Mutations and Information article:

SkepticWiki writes:

Any mutation that lengthens the DNA will increase the number of "bits" in it...

If by "bits" he means a measure of information, then this is by no means always true. It depends upon your message set. For example, let's say this is the set of possible messsages:

  • CAG
  • TAC
  • ACT
  • CAGACT
  • TACGTA
  • ACTCGT

Assume each messages is equally likely. Let's say that our beginning DNA string is TAC and that it experiences a mutation to become TACGTA. Since both TAC and TACGTA are in the message set and are equally likely, no more bits of information are communicated.

You have to keep separate the information from the encoding for the information, which frequently includes redundancy. If you're counting the redundancy then you're overstating the amount of information. In my example the amount of information represented by any one of the DNA strings is log26 or 2.58 bits. Mutating TAC to TACGTA doesn't increase it.

--Percy


This message is a reply to:
 Message 26 by PaulK, posted 10-19-2009 9:54 AM PaulK has responded

Replies to this message:
 Message 28 by PaulK, posted 10-19-2009 10:36 AM Percy has responded
 Message 34 by Dr Adequate, posted 10-19-2009 11:44 AM Percy has responded

    
PaulK
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Posts: 15085
Joined: 01-10-2003
Member Rating: 3.3


Message 28 of 80 (531671)
10-19-2009 10:36 AM
Reply to: Message 27 by Percy
10-19-2009 10:17 AM


Re: Quantification
The section you quote actually precedes the argument that Dr Adequate refers to (labelled "Problem 2: A Mathematical Argument") which partly explains your problem.

I think that the specific point you object to refers to a straight binary encoding, rather than your arbitrary selection of "messages".


This message is a reply to:
 Message 27 by Percy, posted 10-19-2009 10:17 AM Percy has responded

Replies to this message:
 Message 29 by Percy, posted 10-19-2009 10:55 AM PaulK has responded

    
Percy
Member
Posts: 18498
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.9


Message 29 of 80 (531677)
10-19-2009 10:55 AM
Reply to: Message 28 by PaulK
10-19-2009 10:36 AM


Re: Quantification
PaulK writes:

The section you quote actually precedes the argument that Dr Adequate refers to (labelled "Problem 2: A Mathematical Argument") which partly explains your problem.

Well, I'll try to slog on, but to the extent that his conclusions depend upon faulty assumptions they will in turn be faulty.

I think that the specific point you object to refers to a straight binary encoding, rather than your arbitrary selection of "messages".

There's no such thing as a "straight binary encoding." This becomes obvious when one tries to answer the question, "What is the straight binary encoding of 1.585 bits of information?" The theoretical amount of information rarely has any precise encoding in an integer number of bits, and the excess number of bits are redundant.

It feels to me like this is a case of trying to make into a general principle something that is not always true.

--Percy


This message is a reply to:
 Message 28 by PaulK, posted 10-19-2009 10:36 AM PaulK has responded

Replies to this message:
 Message 30 by PaulK, posted 10-19-2009 11:13 AM Percy has responded

    
PaulK
Member
Posts: 15085
Joined: 01-10-2003
Member Rating: 3.3


Message 30 of 80 (531680)
10-19-2009 11:13 AM
Reply to: Message 29 by Percy
10-19-2009 10:55 AM


Re: Quantification
quote:

Well, I'll try to slog on, but to the extent that his conclusions depend upon faulty assumptions they will in turn be faulty.

The relevant section is short and largely self-contained. I think that you are pretty much wasting your time trying to critique the other sections.

quote:

There's no such thing as a "straight binary encoding."

That is a weird thing to say. Of course you can produce a straight binary encoding of a DNA sequence. SImply assign a distinct pair of bits to each of the 4 possible bases.


This message is a reply to:
 Message 29 by Percy, posted 10-19-2009 10:55 AM Percy has responded

Replies to this message:
 Message 33 by Percy, posted 10-19-2009 11:40 AM PaulK has responded

    
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