Re: [asa] Information and knowledge

The sequence itself is shannon information because it's just a sequence of
ACTG. Note Randy:

> Information about the genome and its sequence of course is classical
information. This is transmitted.

If the receiver is a computer then Shannon applies if the receiver is
biological it doesn't. That's because genetic engineering techniques does a
transform of the DNA before replication.

Take another example. If I take a digital photograph of a pen and transmit
it over the net then information is transmitted in the Shannon sense. Does
the pen itself have information? Nope because the pen does not get
reconstructed. Let's say it's computer injection mold instruction for a pen
that get transmitted then the pen would be properly considered the receiver
but not the source The coding must be such to create an exact copy of the
original. So, we can use portions of a DESCRIPTION of the genome to create
proteins. But that's no different than a chemical engineer observing a
reaction transmitting a description of the reaction and having the reaction
replicated.

When Francis Collins uses the phrase the genetic code is the instruction set
for life it's an over-simplified illustration.

On 4/12/07, David Opderbeck <dopderbeck@gmail.com> wrote:
>
> *Genetic information is transferred through replication, not through
> transmission via a channel. There's a fundamental difference.
> *
> I undertand that is true in an organism qua organism. But genetic
> information *can* be extracted from an organism and transmitted over a
> channel. Look again at that gene synthesis link I posted ( http://www.blueheronbio.com/genemaker/technology.html)
> and note what is happening. Sequence data is extracted from an organism.
> It is transmitted (via a website, no less) to the synthesis company. The
> synthesis company runs it through some computational algorithms and then
> constructs synthetic DNA. The synthetic DNA can be used, say, to "instruct"
> a cloned microorganism to express an enzyme that digests chemical waste.
>
> It seems to me that this is a quite clear example of genetic information
> being transmitted over a channel. It is a set of instructions that people
> are sending around, manipulating, and than inserting into the "hardware"
> ("wetware") of a clone as instructions for what functions the clone must
> perform.
>
> I get the sense that you all "protest too much" to the notion that genetic
> information can be Shannon information because of the ID implications of
> that notion.
>
> Or maybe I'm being completely dense. How is extracting a gene sequence
> into a set of A,C,T, and G's, transmitting that data over the internet, and
> then reassembling it into a biological substrate for insertion into a clone
> not the transmission of "information?"
>
> As far as I know, which I admit isn't very far, the concept of Shannon
> information is employed widely in biotechnology and bioinformatics.
>
> See, e.g., this paper:
> http://ieeexplore.ieee.org/Xplore/login.jsp?url=/iel5/9262/29416/01332413.pdf
> :
>
>
> *Shannon information in complete genomes
> *Chang-Heng Chang; Li-Ching Hsieh; Ta-Yuan Chen; Hong-Da Chen; Liaofu Luo;
> Hoong-Chien Lee
> Computational Systems Bioinformatics Conference, 2004. CSB 2004.
> Proceedings. 2004 IEEE
> Volume , Issue , 16-19 Aug. 2004 Page(s): 20 - 30
> Digital Object Identifier 10.1109/CSB.2004.1332413
> *Summary:* Shannon information in the genomes of all completely sequenced
> prokaryotes and eukaryotes are measured in word lengths of two to ten
> letters. It is found that in a scale-dependent way, the Shannon information
> in complete genomes are much greater than that in matching random sequences
> - thousands of times greater in the case of short words. Furthermore, with
> the exception of the 14 chromosomes of Plasmodium falciparum, the Shannon
> information in all available complete genomes belong to a universality class
> given by an extremely simple formula. The data are consistent with a model
> for genome growth composed of two main ingredients: random segmental
> duplications that increase the Shannon information in a scale-independent
> way, and random point mutations that preferentially reduces the larger-scale
> Shannon information. The inference drawn from the present study is that the
> large-scale and coarse-grained growth of genomes was selectively neutral and
> this suggests an independent corroboration of Kimura's neutral theory of
> evolution.
>
>
>
>
> On 4/12/07, Randy Isaac <randyisaac@comcast.net> wrote:
> >
> > I used the word "teleportation" too loosely for you to extract all
> > that. Strictly speaking, teleportation involves coherence over a long
> > distance between entangled quantum systems so that there is a one-to-one
> > correlation of the states of the relevant particles. I shouldn't have tried
> > to extrapolate the meaning. It's just an analogy there.
> >
> > To be honest, I don't know what you are saying here. (not sure I know
> > what I'm saying either, for that matter!!) Let me try again.
> >
> > It may be useful to think of the various types of 'information.' The
> > word is often used indiscriminately. Three of the different uses of the word
> > are:
> >
> > 1. Information capability or capacity. This would be the total number
> > of physical elements which can embody information. Like 80GB on your hard
> > drive. Or 10^80 as the amount of information in the universe since that is
> > the number of fundamental particles thought to be in the universe (or at
> > least it was way back when I went to school)
> >
> > 2. Information as meaning or a message. This is the message that is
> > being conveyed through some physical channel.
> >
> > 3. Information as complexity. This is the configuration of a physical
> > entity, not the meaning or message ascribed to it. The amount of information
> > required to describe a physical configuration is a measure of its
> > complexity. The description should not be confused with the complexity of
> > the system itself.
> >
> >
> > My point about genetic 'information' vs message 'information' is as
> > follows:
> >
> > Genetic information is really complexity. It is a particular
> > configuration. This should not be confused with our description of that
> > complexity. Any computer code or information transmitted by sentient beings,
> > human or otherwise, involves assigning a meaning to a particular physical
> > configuration. That is fundamentally different from the genetic code where a
> > particular physical configuration has a function but not an assigned
> > meaning.
> >
> > Genetic information is transferred through replication, not through
> > transmission via a channel. There's a fundamental difference. Shannon talks
> > about noisy channels and limits of information transfer through those
> > channels. Genetic replication is quite different and doesn't follow those
> > theorems.
> >
> > To me, the conclusion of all this is that genetic information, while
> > having a lot of similarities to anthropogenic computer code, is
> > fundamentally different from any information transmitted by sentient beings.
> > It is therefore not appropriate to infer an intelligent designer from an
> > analogy between genetic information and human information.
> >
> >
> >
> > Randy
> >
> >
> > ----- Original Message -----
> > *From:* David Opderbeck <dopderbeck@gmail.com>
> > *To:* Randy Isaac <randyisaac@comcast.net>
> > *Cc:* asa@calvin.edu
> > *Sent:* Thursday, April 12, 2007 9:33 AM
> > *Subject:* Re: [asa] Information and knowledge
> >
> >
> > Randy said: *Your sci-fi example doesn't negate the argument. What you
> > describe is really teleportation, in a sense. Information about the genome
> > could in principle be sufficiently complete that it could be reconstructed.
> > That information which is teleported is indeed Shannon-information. The DNA
> > itself isn't information of that type.
> > *
> > Maybe I'm being dense, but this seems to me different only in degree
> > from the notion of Shannon information in computing. My laptop's hard
> > drive comprises a platter with of many small magnetic regions that encode
> > bits of data. Those bits of data can be extracted from the platter /
> > magnetic medium and transferred to an array of transistor cells on my USB
> > flash drive. The same bits of data can be extracted from the flash chip and
> > transferred onto the capacitors of the temporary DRAM memory on the
> > workstation in a classroom. Then I can teach a class, and hopefully,
> > between students dozing, IM'ing, surfing the web, and daydreaming, at least
> > some of the same data can be transferred into the "wetware" medium of my
> > student's brains.
> >
> > Certainly I haven't in this process reconstructed *all* the information
> > on my laptop's hard drive and transferred it to my student's brains -- not
> > even all the information that was on my hard drive concerning my lecture,
> > since at least some of the laptop-resident information is specific to the
> > medium on which it resides. But, from the perspective of information
> > theory, I don't think you'd say I merely "teleported" my lecture from the
> > laptop to my students. There was a relatively lossless transfer of some
> > information over a series of communications channels.
> >
> > Likewise, I don't see why extracting information from a genetic sequence
> > -- say, a group of genes responsible for regulating the expression of an
> > enzyme that breaks down industrial waste -- transferring that information to
> > a computer medium, and then "printing" that information to a set of
> > synthetic genes for insertion into a biological waste management device,
> > would be a form of "teleportation" rather than a transfer of Shannon
> > information across a communications channel to different media. I don't see
> > why this would be merely a transfer of information "about" a genome any more
> > than taking my lecture notes off of the hard drive and teaching a class
> > would be merely a transfer of information "about" my brain or my hard drive
> > -- unless the whole project of information theory is simply misplaced as an
> > ontological matter. (I also don't think, BTW, that the wetware "printer" is
> > entirely in the realm of science fiction anymore.)
> >
> > On 4/9/07, Randy Isaac <randyisaac@comcast.net> wrote:
> > >
> > >
> > > Dave,
> > > The argument is a little different from what you are citing. I'm
> > not saying that genetic information isn't Shannon-type information because
> > it isn't medium-independent. Rather, it isn't medium-independent because it
> > isn't Shannon-information. That is merely the easiest way to see the
> > ramification of it. It's the fundamental definition of information and
> > complexity. Complexity can be thought of as the amount of information
> > required to describe an object or any entity. Complexity even applies to
> > information itself. Data compression is least efficient in the most complex
> > information streams. The so-called genetic code is the information we use to
> > describe the genome.
> > >
> > > Your sci-fi example doesn't negate the argument. What you describe
> > is really teleportation, in a sense. Information about the genome could in
> > principle be sufficiently complete that it could be reconstructed. That
> > information which is teleported is indeed Shannon-information. The DNA
> > itself isn't information of that type.
> > >
> > > The novelty of DNA is that, unlike virtually everything else in
> > our universe, it is self-replicating. That replication, with an
> > infinitesimal but non-zero error rate, is incredibly potent as a means for
> > generating additional complexity. Other inanimate objects can and do also
> > become more complex--that's entropy, if you will--but nothing comes close to
> > the effectiveness of self-replication.
> > >
> > > Randy
> > >
> > > ----- Original Message -----
> > > From: David Opderbeck
> > > To: Randy Isaac
> > > Cc: asa@calvin.edu
> > > Sent: Sunday, April 08, 2007 7:40 PM
> > > Subject: Re: [asa] Information and knowledge
> > >
> > >
> > > Randy, I think you're alluding here to a really important and usually
> > overlooked aspect of the ID discussion: the ontology of information. Bill
> > Dembski, following in the footsteps of communications and cybernetics
> > theorists who've built on Shannon, views information as a sort of ontic
> > entity apart from matter and energy (at least that is how I understand the
> > implications of Dembski's ideas). This idea can't be dismissed lightly --
> > it is being built into a discipline, the Philosophy of Information, that has
> > nothing to do with ID, and it underlies much contemporary sociological and
> > legal theory concerning social norms and law regarding communications, the
> > Internet, and other types of information.
> > >
> > > Personally, my present view is that it's misguided to think of
> > information as something ontologically separate from matter and energy. I
> > think this reflects a sort of Cartesian dualism that I'm keen to avoid in
> > both theology and legal theory. But I'm not so sure its as simple
> > as arguing that genetic information isn't Shannon information just because
> > genetic information doesn't appear at present to be medium-independent.
> > It's not impossible to imagine a biotechnology scenario in which genetic
> > information can be extracted from an organismal genome, stored on a
> > computing device, and then "printed" to a "wet ware" printer to produce a
> > synthetic medicine, body part, organism, etc. After all, whod've thunk
> > fifty years ago that today we'd be walking around with gigabytes of data on
> > pocket flash drives?
> > >
> >
> >
> >
> >
>

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Received on Thu Apr 12 19:37:43 2007