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Author Topic:   Evolving New Information
Percy
Member
Posts: 18309
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.7


Message 406 of 458 (543678)
01-20-2010 8:13 AM
Reply to: Message 405 by Taq
01-19-2010 6:59 PM


Re: What is information?
Taq writes:

I would add a 3rd option as the most important. Since DNA is always spoken of as a code with four letters, 3 codons, and so forth it is important to relate these to the actual chemical reactions.

You're going to have to connect the dots for me on this one. The actual machinery that implements the information communication channels is unimportant at an information theoretic level.

You've added a bit more detail and used different names, but it seems like much the same thing. We could break it down the processes in which information from DNA is the driving element like this:

  1. Cell metabolism.
  2. Body metabolism.
  3. Heredity.

--Percy


This message is a reply to:
 Message 405 by Taq, posted 01-19-2010 6:59 PM Taq has not yet responded

    
LucyTheApe
Inactive Member


Message 407 of 458 (543831)
01-21-2010 7:59 AM
Reply to: Message 403 by Percy
01-18-2010 7:11 AM


Re: What is information?
Percy writes:

Since LucyTheApe is apparently going to take their time replying, I'd like to respond to this:

Sorry Percy but time is relative. Also I apologise for posting on the wrong thread.

I believe the cell is the interpreter/decoder. Where it and the dna code comes from is in dispute; design/nature. If you try to put chicken nucleus into a human egg cell, the cell will try to produce a human, not a chicken. Similarly if you put human dna in a chicken egg, the egg will try produce a chicken, not a human. The cell contains its own information.

Also the amount of information is not necessarily linearly related to the meaning of that information. Different communication systems use different coding.

In my analogy the environment for my code is the java interpreter; the shell (852 bits) tells the interpreter that it is a program (egg); a java application.



public static void main(String args){}


The shell is a standarized connection/access protocol. If the interpreter can't establish that the egg is compliant then it should abort it. Or similarly
In expert systems, a shell is a piece of software that is an "empty" expert system without the knowledge base for any particular application.

Once it is established the program is legitimate, then the program (cell) does its stuff.

So my particular cell wants to juggle a couple of objects (X bits) or it wants to juggle three objects (x + y bits).

The code then is a data base of methods or instructions for doing different things.

Let me try to illustrate this:


You then have to consider this:

Both these systems are top down structures. There is no way that natural laws can produce a coding system that complies with the requirements of this system. You can not impose code on the interpreter.

I'll reply to your other comments shortly.


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

blɛz paskal


This message is a reply to:
 Message 403 by Percy, posted 01-18-2010 7:11 AM Percy has responded

Replies to this message:
 Message 409 by Percy, posted 01-21-2010 8:35 AM LucyTheApe has responded
 Message 424 by Iblis, posted 01-22-2010 4:18 PM LucyTheApe has not yet responded

  
LucyTheApe
Inactive Member


Message 408 of 458 (543839)
01-21-2010 8:28 AM
Reply to: Message 404 by Percy
01-19-2010 7:23 AM


Re: What is information?
Percy writes:

For some reason you keep popping in and out every month or three, and now you're apparently doing it again, so here's some additional information that may help break this pattern.

I've got a life.

Percy writes:

People don't believe you know much about information theory because you've demonstrated your lack of knowledge over and over again. You appear to be trying to solve the problem of how to win a debate on a topic you know little about, and so you've adopted this strange strategy of "post a couple messages then exit for a couple months."


  1. I don't give a fat rats arse what people think.
  2. I know little about information theory? There's nothing to know except the equation which shows that information is not the normal state.

Percy writes:

So you're going to have to explain how you calculated the amount of information in your programs. When you finally admit to yourself that you can't do it (something that everyone following this discussion already realizes), only then will we be able to make progress.

Let me try again.


  1. Shell = "public static void main string args(){dna code here}"

  2. shuffle two objects = however many bits the interpreter told me there are.

  3. Shuffle three objects = however many bits the interpreter told me there were.

The amount of additional information = 3-2, how difficult is that to understand?

Now we all agree that information is a surprise effect right? Then try remove or change one of these bits and keep the program working.

You should be able to modify the code bit by bit, keep the program readable, and add new information. You can't.


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

blɛz paskal


This message is a reply to:
 Message 404 by Percy, posted 01-19-2010 7:23 AM Percy has acknowledged this reply

  
Percy
Member
Posts: 18309
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.7


Message 409 of 458 (543843)
01-21-2010 8:35 AM
Reply to: Message 407 by LucyTheApe
01-21-2010 7:59 AM


Re: What is information?
LucyTheApe writes:

Percy writes:

For some reason you keep popping in and out every month or three, and now you're apparently doing it again...

I've got a life.

Having a life is consistent with the delay, but not with the constant attempts to avoid explaining how you calculated your information values. Put them together and it adds up to evasion.

LucyTheApe writes:

In my analogy the environment for my code is the java interpreter; the shell (852 bits) tells the interpreter that it is a program (egg); a java application.

How did you calculate the figure of 852 bits?

--Percy


This message is a reply to:
 Message 407 by LucyTheApe, posted 01-21-2010 7:59 AM LucyTheApe has responded

Replies to this message:
 Message 411 by LucyTheApe, posted 01-21-2010 11:06 AM Percy has responded

    
LucyTheApe
Inactive Member


Message 410 of 458 (543847)
01-21-2010 9:01 AM
Reply to: Message 402 by greyseal
01-17-2010 4:00 PM


Re: What is information?
greyseal writes:

lucy, I have not forgotten that I asked you to define information for us - specifically how you calculate it - and that you still have not done so in any meaningful way when dealing with genetics.

Why ask an ignoramus?

But anyway I'll tell you what I think. As I have said before, information is a coded message. One way of measuring that information is by using bits. That doesn't mean to say that the same message always uses the same amount of bits in every communication system; it doesn't.

Computers are very simple machines. The cell isn't. The cell doesn't use a binary system at all, but a very sofisticated "fuzzy" quaternary system. A system that is as yet not understood.

You say that you have shown me an increase in information within a cell. I'm sorry I can't remember, but after I have posted this I will go back and check. Although I'm sure I would have read it on the front page of Nature if it were true. I won't comment further on this, instead I will re-read your reference.

greyseal writes:

Don't think I didn't notice when you said that an increased amount of bits for your modified shell program counted as "new information", but that you also flatly said "No, that's how you're defining information, not me." to the question "You think the amount of information in a program is equal to the number of bits output by its compiler?" - which is exactly what you WERE saying.

You're taking me out of context greyseal. The trick in measuring information content is to see if you could re-write the code, or remove symbols without affecting the meaning of the message. I am not saying that my code, in any sense, is the most efficient way of communicating the message. I bet I (or someone else here) could rewrite the code using less bits.

Edited by LucyTheApe, : typo


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

blɛz paskal


This message is a reply to:
 Message 402 by greyseal, posted 01-17-2010 4:00 PM greyseal has responded

Replies to this message:
 Message 414 by greyseal, posted 01-21-2010 12:14 PM LucyTheApe has responded

  
LucyTheApe
Inactive Member


Message 411 of 458 (543862)
01-21-2010 11:06 AM
Reply to: Message 409 by Percy
01-21-2010 8:35 AM


Re: What is information?
Percy writes:

How did you calculate the figure of 852 bits?

Here, you work it out.


Or take my word for it.


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

blɛz paskal


This message is a reply to:
 Message 409 by Percy, posted 01-21-2010 8:35 AM Percy has responded

Replies to this message:
 Message 412 by Percy, posted 01-21-2010 11:12 AM LucyTheApe has responded

  
Percy
Member
Posts: 18309
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.7


Message 412 of 458 (543863)
01-21-2010 11:12 AM
Reply to: Message 411 by LucyTheApe
01-21-2010 11:06 AM


Re: What is information?
Hi LucyTheApe,

Using this image that you provided:

Please describe for us how you calculate an information content of 832 bits.

--Percy


This message is a reply to:
 Message 411 by LucyTheApe, posted 01-21-2010 11:06 AM LucyTheApe has responded

Replies to this message:
 Message 413 by LucyTheApe, posted 01-21-2010 11:32 AM Percy has responded

    
LucyTheApe
Inactive Member


Message 413 of 458 (543868)
01-21-2010 11:32 AM
Reply to: Message 412 by Percy
01-21-2010 11:12 AM


Re: What is information?
Percy writes:

Please describe for us how you calculate an information content of 832 bits.

Do we have to go on about this Percy: take a copy of this code and compile it:


public class information{

public static void main(String args) {

}}


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

blɛz paskal


This message is a reply to:
 Message 412 by Percy, posted 01-21-2010 11:12 AM Percy has responded

Replies to this message:
 Message 415 by greyseal, posted 01-21-2010 12:18 PM LucyTheApe has not yet responded
 Message 416 by Percy, posted 01-21-2010 2:47 PM LucyTheApe has not yet responded

  
greyseal
Member (Idle past 1938 days)
Posts: 464
Joined: 08-11-2009


Message 414 of 458 (543870)
01-21-2010 12:14 PM
Reply to: Message 410 by LucyTheApe
01-21-2010 9:01 AM


Re: What is information?
But anyway I'll tell you what I think. As I have said before, information is a coded message. One way of measuring that information is by using bits. That doesn't mean to say that the same message always uses the same amount of bits in every communication system; it doesn't.

Computers are very simple machines. The cell isn't. The cell doesn't use a binary system at all, but a very sofisticated "fuzzy" quaternary system. A system that is as yet not understood.

So your answer to "what is information?" in the context of cells and genetics is:

"I don't actually know"

thanks!

Your answer to "how do you calculate the amount of information in the cell" is:

"count the number of bits"

Thanks!

If I'm wrong, tell me what your answer is, not what it isn't.

You say that you have shown me an increase in information within a cell. I'm sorry I can't remember, but after I have posted this I will go back and check.

I wasn't the only one to give you this example - and infact there were far more detailed examples than I gave you.

Simply, the examle given was a hypothetical (but valid) known species with only three alleles in the population, to which a coding error is made resulting in four alleles.

An actual living example is the peppered moth, other examples include carrots that aren't orange and bananas that are yellow.

The example that covers your natural occurence increasing the size of the genome was a massive, massive coding error where entire sections of code were copied - in this particular case it caused far more problems than it solved, but like tiktaalik and archy it shows that such a thing is possible. There are other examples but they are far beyond my capability to properly explain. RAZD and Wounded King have though, I believe.

The trick in measuring information content is to see if you could re-write the code, or remove symbols without affecting the meaning of the message.

No, it isn't. You are dead wrong.

cheers,

Daniel.


This message is a reply to:
 Message 410 by LucyTheApe, posted 01-21-2010 9:01 AM LucyTheApe has responded

Replies to this message:
 Message 419 by LucyTheApe, posted 01-22-2010 8:42 AM greyseal has responded

    
greyseal
Member (Idle past 1938 days)
Posts: 464
Joined: 08-11-2009


Message 415 of 458 (543871)
01-21-2010 12:18 PM
Reply to: Message 413 by LucyTheApe
01-21-2010 11:32 AM


Re: What is information?
Percy writes:

Please describe for us how you calculate an information content of 832 bits.

Do we have to go on about this Percy: take a copy of this code and compile it:


public class information{

public static void main(String args) {

}}

The section I have highlighted tells everyone that the way you calculated the amounts of information was the count the bits.

Ergo, you are defining information in amount of bits - possibly valid, but pokes holes in most of your objections and ignores the possibility of having errors in the code that work producing the same number of bits (i.e. new alleles).


This message is a reply to:
 Message 413 by LucyTheApe, posted 01-21-2010 11:32 AM LucyTheApe has not yet responded

    
Percy
Member
Posts: 18309
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.7


Message 416 of 458 (543883)
01-21-2010 2:47 PM
Reply to: Message 413 by LucyTheApe
01-21-2010 11:32 AM


Re: What is information?
LucyTheApe writes:

Percy writes:

Please describe for us how you calculate an information content of 832 bits.


Do we have to go on about this Percy: take a copy of this code and compile it:

public class information{

public static void main(String args) {

}}

As I explained back in Message 367, the size of the file output by a compiler is not a measure of a program's information. The size of that output file will vary by compiler version and platform, but the amount of information in your program must be a constant, so obviously compiler output is not a measure of information.

You're obviously very confused. First you claimed that you used a compiler to calculate the information, then in response to my explanation that this is not a method by which one can measure information you denied using a compiler and accused me making that erroneous claim, then you became evasive for several months, and now you're claiming you used a compiler again.

You can't use a compiler to calculate the amount of information in a computer program. An accurate calculation would be a very complicated exercise. A compiler is really just a translator from one language (the computer programming language) to another language (the binary instructions of a computer's CPU).

You need to either present an example simple enough that you can calculate the amount of information, or accept the example I presented earlier in this thread, which has the additional advantage of using real DNA nucleotides and codons, see Message 1.

--Percy


This message is a reply to:
 Message 413 by LucyTheApe, posted 01-21-2010 11:32 AM LucyTheApe has not yet responded

Replies to this message:
 Message 417 by greyseal, posted 01-22-2010 1:13 AM Percy has acknowledged this reply

    
greyseal
Member (Idle past 1938 days)
Posts: 464
Joined: 08-11-2009


Message 417 of 458 (543927)
01-22-2010 1:13 AM
Reply to: Message 416 by Percy
01-21-2010 2:47 PM


that's a pretty impressive amount of evasion!
You need to either present an example simple enough that you can calculate the amount of information, or accept the example I presented earlier in this thread, which has the additional advantage of using real DNA nucleotides and codons, see Message 1

so let me get this straight - LTA is so oblivious to the meaning of information that it's taken 416 messages for her to get the problems with her ideas?

that after 416 messages, she still hasn't understood the very first message in this thread?

...is there an award for that?


This message is a reply to:
 Message 416 by Percy, posted 01-21-2010 2:47 PM Percy has acknowledged this reply

Replies to this message:
 Message 418 by Huntard, posted 01-22-2010 4:05 AM greyseal has not yet responded

    
Huntard
Member (Idle past 371 days)
Posts: 2870
From: Limburg, The Netherlands
Joined: 09-02-2008


Message 418 of 458 (543932)
01-22-2010 4:05 AM
Reply to: Message 417 by greyseal
01-22-2010 1:13 AM


Re: that's a pretty impressive amount of evasion!
And this is not even the first thread about information Lucy's been in.
This message is a reply to:
 Message 417 by greyseal, posted 01-22-2010 1:13 AM greyseal has not yet responded

    
LucyTheApe
Inactive Member


Message 419 of 458 (543949)
01-22-2010 8:42 AM
Reply to: Message 414 by greyseal
01-21-2010 12:14 PM


Re: What is information?
greyseal writes:

So your answer to "what is information?" in the context of cells and genetics is:

"I don't actually know"

The amount of information in the dna and mdna, I suspect, is related to the number of base pairs.

greyseal writes:

Simply, the examle[sic] given was a hypothetical...

The entire TOE is hypothetical...please.

greyseal writes:

..but like tiktaalik and archy it shows that such a thing is possible

Tiktaalik is a fish and archaeopteryx is a bird. There is not one single shred of evidence that they had a baby that was an amphibian or that their parent was a dinosaur, respectively. Any suggestion is pure speculation.

LTA writes:

The trick in measuring information content is to see if you could re-write the code, or remove symbols without affecting the meaning of the message.

greyseal writes:

No, it isn't. You are dead wrong.

And you can show me how I'm wrong, right?

Percy writes:

As I explained back in Message 367, the size of the file output by a compiler is not a measure of a program's information.

I disagree with you Percy. Let me get this right; reality is information and compiled code isn't..hmm.

If you change the communication system then you can reduce the amount of information required to pass on the same message, just like a new version of the compiler or a new release of a language.

Percy writes:

You can't use a compiler to calculate the amount of information in a computer program.

Yes you can, that's what I have done. And as I said to greyseal it doesn't mean that my code is the most sophisticated or efficient way of passing a message; it could be rewritten more efficiently, with less information.

And I haven't be evading anything. My absence from the forum has nothing to do with this thread.


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

blɛz paskal


This message is a reply to:
 Message 414 by greyseal, posted 01-21-2010 12:14 PM greyseal has responded

Replies to this message:
 Message 420 by greyseal, posted 01-22-2010 9:40 AM LucyTheApe has responded
 Message 422 by Percy, posted 01-22-2010 11:14 AM LucyTheApe has not yet responded
 Message 423 by Taq, posted 01-22-2010 4:07 PM LucyTheApe has not yet responded
 Message 425 by Percy, posted 01-23-2010 5:45 PM LucyTheApe has responded

  
greyseal
Member (Idle past 1938 days)
Posts: 464
Joined: 08-11-2009


Message 420 of 458 (543952)
01-22-2010 9:40 AM
Reply to: Message 419 by LucyTheApe
01-22-2010 8:42 AM


Re: What is information?
Percy writes:

You can't use a compiler to calculate the amount of information in a computer program.

Yes you can, that's what I have done.

no, you haven't. As Percy stated, if different compilers take the same code and create files of different sizes using different code, and you claim that simply "counting the bits" tells you how much information there is in those files, then you are dead wrong.

The size of the files may be related to the amount of information, but it is not dependant on it - this is the key objection Percy has.

Similarly, you are probably correct when you say

The amount of information in the dna and mdna, I suspect, is related to the number of base pairs
but that doesn't change the fact that your answer to what it is is "I don't actually know", neither do you know how to quantify or measure it.

A new allele may not increase the size of an organism's genetic code, but it does increase the size of the pool.


This message is a reply to:
 Message 419 by LucyTheApe, posted 01-22-2010 8:42 AM LucyTheApe has responded

Replies to this message:
 Message 421 by LucyTheApe, posted 01-22-2010 10:01 AM greyseal has not yet responded

    
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