Re: [asa] Information and knowledge

*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.*

But so does a computer. Even if the information is transmitted from one
computer to another, it comes off of one kind of medium (say, a hard drive)
and may end up in a different kind of medium (say, a flash drive -- or a
human brain). The computer / biological distinction seems completely
arbitrary to me.

*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.*
**
Let's say a device takes a three dimensional scan of the pen all the way
down to the molecular level, the scan data is uploaded to a computer and fed
to a three-dimensional printer, and another pen is "printed." It's not
teleportation because the original pen still sits on the desk; now there are
two pens, the original and a copy. It seems to me the pen is then the
source and the receiver. (So, ok, we don't have Star Trek replicators yet,
but we do have 3D scanners that will scan an object into CAD software and 3D
"printers" that will fabricate a tangible object from the CAD design, so the
concept isn't necessarily impossible.)

*We object to ID because it misapplies information theory.*

I don't necessarily disagree with you here, but I think I disagree with your
reasons. Your reasons seem to be an a priori assumption -- that we can't
admit to a "coder" of biological information in DNA but rather we must
understand DNA as something entirely material. Of if not -- what am I
missing?

My objection is that information theory *in general* is taken too far when
it leads to the view that information is truly ontologically a separate,
medium-independent property.

On 4/12/07, Rich Blinne <rich.blinne@gmail.com> wrote:
>
> 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
> > > To: Randy Isaac
> > > 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?
> > > >
> > >
> > >
> >
> >
>
>

To unsubscribe, send a message to majordomo@calvin.edu with
"unsubscribe asa" (no quotes) as the body of the message.
Received on Thu Apr 12 20:56:44 2007