Re: [asa] None Standard Information (Theory) in ID

David:

You speak of partition functions as possibly providing a deeper
understanding of the evolutionary process.
A partition function expresses the probability of various states
under certain canonical, or idealized, situations.
The entire mathematical process is enslaved to a kind of idealized
model of the "real" world of "particles," usually a "large"
number of them.

Information, as it has always been spoken of in ID, is not probabilistic.
It is about meaning, not the mere encoding of meaning (e.g., Shannon
information).

So how does a partition function relate to this kind of information?
The meaning in a cell is encoded in the alphabet of amino acids.
The partition function governs, not the meaning or code, but the
media in which the meaning is encoded.

Meaning appears to not be physical and therefore not governed by partition
functions. Somehow the meaning could be hidden in various initial conditions,
presenting "new" canonical situations and possibilities. The laws of statistics
and of physical laws are never sufficient to explain what is.

Can you say more of what you are thinking here with regard to partition functions?
It seems that the very notion of partition functions, or at least our ability to
be able to construct them, speak of a host of independent particles.
Whereas, information speaks not of independence but of a coherence that binds the
independence into a whole. In some sense, when we speak of statistical systems as
"seeking" minimums of free energy and the like this may be closer to information,
if we could get a handle on what "seeking" means.

Finally, you say,
"A cell isn't just biology. Its really chemical
engineering. And that mathematics is what governs populations of
molecules everywhere - organic or inorganic. Do you disagree?"

Wow! What a statement. I suggest you read this carefully.
A cell isn't only about biology, but it is *really* about chemical
engineering!? Isn't what you really mean is that a cell isn't
about biology at all, but about chemistry? Biology is reducible to
chemistry? And *mathematics* is what governs the chemistry.
Is this a form of Platonism, where the forms govern the instances?

I'm joking in part. I'm pretty sure you didn't intend to say just
this. I was just struck with what it literally seems to say.

bill

On Sat, 21 Nov 2009 18:30:31 +1800, David Clounch <david.clounch@gmail.com> wrote:
>>In my mind I relate the information that Meyers is talking about to the
> functional content of a working program of say a couple of hundred
> thousand
> lines of Fortran code. Lets assume that we have another really smart
> program
> that compresses the Fortran source as much as possible. This means that
> dead
> code is eliminated, comments go, variable names are shortened and on and
> on
> applying language rules till all the redundancy in the program is gone and
> the program is totally unreadable by humans.
>
> Surely it is XML. ;)
>
> And in that case it would be bloatware. I remember ganglia sending a
> megabyte size packet, but the data content was only about 30 bytes. XML
> is
> now being used as a data transport. And that goes to show software
> engineers
> are idiots. XML is great as a declarative specification/configuration
> language. But its not for humans when in a datastream.
>
>
>>Now we compress what is left using the normal compression tools, although
> I
> wonder how much compression one would get.
>
> Well, mr. huffman sez it will get larger. Been there, done that. Seen
> it
> in action.
>
>
> The rest of your post is about specification, not complexity. Anti-ID
> people know one word: complexity. They don't _seem_ to talk about
> specification. Am I wrong?And nobody talks about partition functions.
> Why
> partition functions? Because chemical engineering is based on statistics.
> In my view a mutation isn't sufficient. It needs other parts. Parts that
> are produced by previous mutations but which may not be used until a later
> mutation comes along. So its the concatenation of mutations that counts.
> That spells a re-writing of the partition functions in the equations that
> govern the physics. A cell isn't just biology. Its really chemical
> engineering. And that mathematics is what governs populations of
> molecules
> everywhere - organic or inorganic. Do you disagree?
>
>
>
>
> On Sat, Nov 21, 2009 at 5:56 PM, Dave Wallace
> <wmdavid.wallace@gmail.com>wrote:
>
>> Rich
>>
>> I am about half way through reading Signature in the Cell by Dr. Stephen
>> Meyer. He takes very great pains to indicate that what he is talking
> about
>> is not communications channel capacity and he does not mention
> compression
>> or other aspects of Information Theory at all, at least as far as I have
>> read. He specifically says that what he is talking about is not Shannon
>> information. As best I understand him, he is talking about a functional
>> design specification at the most basic reduced level.
>>
>> From your online discussion with Del Tackett
>> Rich Blinne on May 22nd, 2008 10:16 pm
>>
>>> It is also presumed that DNA is a design specification. A more complex
>>> design requires a more complex specification. But, there are two
> paradoxes
>>> in biology known as the c-value and g-value paradoxes. More complex
> life
>>> does not necessarily have a higher DNA weight nor higher numbers of
> gene.
>>> The Human Genome Project overestimated the number of genes going in
> with
>>> estimates of 80-140,000 genes when the real number is around 30,000.
> What’s
>>> going on is there is a lot of “random” alternative splicing
> producing
>>> multiple proteins from the same gene. Before you say a ha, note that
> humans
>>> do not have the record for alternative splicing. The fruit fly does
> with
>>> 38,000 splice variants. Thus, evolution does not need to generate new
>>> “information” because ID’s concept of information is simply
> flawed.
>>>
>>
>> In my mind I relate the information that Meyers is talking about to the
>> functional content of a working program of say a couple of hundred
> thousand
>> lines of Fortran code. Lets assume that we have another really smart
> program
>> that compresses the Fortran source as much as possible. This means that
> dead
>> code is eliminated, comments go, variable names are shortened and on and
> on
>> applying language rules till all the redundancy in the program is gone
> and
>> the program is totally unreadable by humans. Now we compress what is
> left
>> using the normal compression tools, although I wonder how much
> compression
>> one would get. As I see it the information the ID folks are talking
> about
>> would be proportional to the final compressed program size plus the
>> restriction that the results computed by the code must be correct ie the
>> chemical strings/proteins in the cell must be able to function/reproduce
>> whatever. Now the older programmers here know that replacing
>>
>> DO 3 I = 1,3
>> by
>> DO 3 I = 1.3
>>
>> could well result in a broken non functional program as a loop is turned
>> into an assignment statement. Thus the compressed size is only part of
> the
>> issue as the program must also function correctly. (note to none
> programmers
>> what I illustrate reflects extremely bad programming language design but
>> when it was designed back in the 1950s people did not know any better,
> it is
>> doubtful that we have come very much further but I won't get started on
> that
>> issue)
>>
>> AFAIK this kind of information is NOT what people talk about in
> Information
>> Theory. Sure the compressed size, transmission characteristics are
> covered
>> in Info Theory but not the requirement to execute properly.
>>
>> It seems to me that the kind of process I have described would get rid
> of
>> the equivalent of spliced variants, none coding regions.... We also know
>> that a totally different algorithm might also produce a properly
> functioning
>> program and have a much shorter length. Thus Meyers is trying to
> estimate
>> the approximately minimal amount of information/machinery needed to make
> the
>> first working cell(s). The complexity is staggering since the
> dependencies
>> are circular. Maybe you don't think so but I do. I think you are being a
>> little unfair to people who are not information theorists and should
>> postulate the most favorable interpretation of their meaning.
>>
>> Dave W
>>
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Received on Sat Nov 21 10:15:31 2009