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Author Topic:   Evolving New Information
slevesque
Member (Idle past 2927 days)
Posts: 1456
Joined: 05-14-2009


Message 106 of 458 (511091)
06-06-2009 2:23 AM


advancement in this debate. Sanford developped along with Baumgardner a computer program named 'Mendel's accountant' which ''is a user-friendly biologically realistic simulation program for investigating the
processes of mutation and selection in sexually reproducing diploid populations''.

(on a side note, Baumgardner is the one who developped the 'Terra' program, used by geophysicists)

Sanford says in an interview that this program has been reported in two secular journals. I'm trying to find the articles in question.

EDIT:

John Sanford, John Baumgardner, Wes Brewer, Paul Gibson, and Walter ReMine, Mendel’s Accountant: A biologically realistic forward-time population genetics program, Scalable Computing: Practice and Experience 8(2):147–165, June 2007.

John Sanford, John Baumgardner, Wes Brewer, Paul Gibson, and Walter ReMine, Using computer simulation to understand mutation accumulation dynamics and genetic load, in Y. Shi et al. (eds.), Computational Science—ICCS 2007, Part II, Lecture Notes in Computer Science 4488, Springer–Verlag, Berlin, Heidelberg, pages 386–392.

They has made simulations using this program that confirmed what Sanford was advancing in his book Genetic entropy.

This is the description of the program, I'm reading it right now. (http://www.scpe.org/vols/vol08/no2/SCPE_8_2_02.pdf)

Edited by slevesque, : No reason given.


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Percy
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Posts: 18872
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


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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Dr Jack
Member (Idle past 392 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 108 of 458 (512242)
06-15-2009 12:05 PM
Reply to: Message 77 by Percy
05-27-2009 8:09 AM


That's fascinating Percy.

Presumably there's also a frequency dependent effect wherby less used codons are translated faster (since there's less competition for the tRNAs used).


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AustinG
Member (Idle past 3455 days)
Posts: 36
Joined: 04-06-2009


Message 109 of 458 (512493)
06-18-2009 1:40 PM


Joining in
Can anyone define information as it pertains to mutations? I'd like to join in on the debate; however, I am not sure I fully understand how the word information is being used.

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Percy
Member
Posts: 18872
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


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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slevesque
Member (Idle past 2927 days)
Posts: 1456
Joined: 05-14-2009


Message 111 of 458 (512685)
06-20-2009 12:59 AM


Didn't Shannon say that his information theory should not be applied to biology, genetics, life or something like that ?

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Percy
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Posts: 18872
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


Message 112 of 458 (512699)
06-20-2009 5:13 AM
Reply to: Message 111 by slevesque
06-20-2009 12:59 AM


You are a veritable font of misinformation.

--Percy


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slevesque
Member (Idle past 2927 days)
Posts: 1456
Joined: 05-14-2009


Message 113 of 458 (512701)
06-20-2009 5:15 AM
Reply to: Message 112 by Percy
06-20-2009 5:13 AM


Yeah, I'm checking that one out ... wasn't sure at the time I wrote that question, even less now since I can't seem to track the source down.

I'll keep looking, but I may have to retrack that question


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slevesque
Member (Idle past 2927 days)
Posts: 1456
Joined: 05-14-2009


Message 114 of 458 (512702)
06-20-2009 5:17 AM
Reply to: Message 112 by Percy
06-20-2009 5:13 AM


One thing I am sure is that your initial definition of information in the context of genetics didn't include the semantic aspect.

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Percy
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Posts: 18872
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


Message 115 of 458 (512704)
06-20-2009 5:29 AM
Reply to: Message 114 by slevesque
06-20-2009 5:17 AM


Here's something Shannon actually did say, it's from his paper A Mathematical Theory of Communication:

Shannon writes:

The fundamental problem of communication is that of reproducing at one point either exactly or approximately a message selected at another point. Frequently the messages have meaning; that is they refer to or are correlated according to some system with certain physical or conceptual entities. These semantic aspects of communication are irrelevant to the engineering problem.

Semantics are not part of information theory.

--Percy


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slevesque
Member (Idle past 2927 days)
Posts: 1456
Joined: 05-14-2009


Message 116 of 458 (512705)
06-20-2009 5:51 AM
Reply to: Message 115 by Percy
06-20-2009 5:29 AM


Semantics is 'irrelevant to the engineering problem', this is different from 'irrelevant to information theory'.

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Percy
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Posts: 18872
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


Message 117 of 458 (512706)
06-20-2009 6:15 AM
Reply to: Message 116 by slevesque
06-20-2009 5:51 AM


You're going to argue about the interpretation of plain English?

Shannon's information theory was proposed as a solution to the engineering problem of communicating information in the presence of noise. There are no semantic aspects to information theory. The only people who think they've come up with theories of information that include semantics are creationists like Dembski, Gitt and Spetner, and they've never bothered to connect their ideas to reality.

But though these people think it is possible to include semantics in a theory of information, even they understand that Shannon information does not include semantics. I couldn't say it any better than creationist Perry Marshall at his Cosmicfingerprints website:

Perry Marshall writes:

Claude Shannon's information theory does not mathematically quantify semantics - because so far as we know it's impossible to do so.

Could I suggest that you reverse the order of your "reply first, research later" approach?

--Percy


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slevesque
Member (Idle past 2927 days)
Posts: 1456
Joined: 05-14-2009


Message 118 of 458 (512707)
06-20-2009 6:22 AM
Reply to: Message 117 by Percy
06-20-2009 6:15 AM


Semantics is not part of Shannon's definition of information, since he was more concerned in transmitting information in a wire then to develop the full idea what is information etc.

Nonetheless, semantics is part of information. I mean, if information was one dimensional as Shannon proposed, then 'I have a black dog' would have less information then ''J'ai un chien noir''. But in reality, these two sentences have the same amount of information for the receiver.


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Percy
Member
Posts: 18872
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.5


Message 119 of 458 (512708)
06-20-2009 6:35 AM
Reply to: Message 118 by slevesque
06-20-2009 6:22 AM


No one's saying there's no such thing as semantic information. Of course semantic information exists.

But Shannon's theory of information does not include semantics. It only covers aspects of information that are quantifiable. You cannot adapt Shannon information to make arguments about semantic information. Anyone making claims about semantic information cannot cite Shannon.

--Percy


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slevesque
Member (Idle past 2927 days)
Posts: 1456
Joined: 05-14-2009


Message 120 of 458 (512792)
06-21-2009 4:25 AM
Reply to: Message 119 by Percy
06-20-2009 6:35 AM


Ok then we agree

BTW I never found that quote where Shannon talks of biological systems. So unless I ever find it in the future, it doesn't exist and I agree I was in error.


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