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Author
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Topic: Shapiro on the Genome
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Mike Gene
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Member # 149
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posted 24. February 2003 08:01
Mesk,
I'm well aware of bioinformatics. But as I said above, "Yes, but keep in mind that it's not simply needing computers and programmers to process the biological information. What's more significant is that the computers and programmers themselves provide very good models for understanding cells."
I further understand that the technological nature of life is not "compelling reason to believe that this is in fact evidence for intelligent design." Nevertheless, it is the very type of evidence that we would expect to see if design were true. It's somewhere amidst the technology that we see the distinction between life and non-life.
Now, it may be true that two or three of us may be ignoring the hypothesis that such technology is the product of natural selection. But we live in a global community where thousands are not, thus the natural selection alternative is under no risk of withering on the vine. The alternative that is being ignored is that of ID.
The fact that the technological aspect of life itself cannot provide "epistemological evidence" for ID does not mean ID theorists need to look elsewhere. As I explained above, it not only means ID has passed an important test of falsification, but it also provides a rich template for a positive expression of ID. If ID develops a track record of success in this regard, perhaps we can return to the issue of whether ID or natural selection best accounts for what is found.
PS: I'm getting close to my self-imposed 50 posting/thread limit, so I'll probably offer only one or two more replies, then change topics.
[ 24. February 2003, 08:02: Message edited by: Mike Gene ]
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Janitor@MIT
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posted 24. February 2003 11:33
“But you are implying that the temporal sequence of application is equivalent to the origins of the ideas. My claim is in two parts: First that humans, over thousands of years, observed themselves and the animal world, and that concepts of engineering and control are derived from those observations.”—gedanken
Your claim is far broader than it appears and I suppose its one for the philosophers and appears to rest on the ambiguity of the “origin of ideas” and “applications.” People used to have the idea that Zeus controlled the weather. But that idea is not a scientific theory of control, meteorology, or biology. As I pointed out the primary source that you have cited doesn’t support your claim, nor do the historians of engineering or biology. The concepts of control and information are derived in engineering from the direct investigation of objects of design and theories formulated on the basis of those observations, and the concepts of control and communication entered biology through those theories—as scientific theories and applications. This is not at all an uncommon temporal sequence. E.g., Newcomen invented the steam engine but not on the basis of his scientific knowledge of thermodynamics. Thermodynamics arose subsequently upon investigating the actual physical principles of the steam engine’s operation. (That’s not to say that people didn’t have notions of heat and its flow, and even scientific theories of such.)
Often people do not understand that engineering is an experimental science that has as its principal object of scientific investigation the very objects we design. They sometimes seem to believe that the natural scientists hand us recipes and prescriptions for design that they have abstracted from nature, and we design and build from physical first principles. We almost never do this.
Molecular biologists’ pre-scientific (and sometimes even poetic) notions of control and communications became scientific only after we (engineers) handed them the recipes and prescriptions. Biologists spent the first half of the 20th century debating amongst themselves whether such hypothesized infophoric entities like “genes” actually had any material existence (!). Or whether or not “genes” and all the other related informational tropes they invoked were “useful fictions.” Exactly because they believed some of the ideas that you are expressing, which were subsequently falsified by the discovery of the DNA code! (An abstract algorithmic representation of the interrelation of physical objects.) Sorry, g, but you seem to be attempting to roll back the clock to the pre-scientific days.
But I’ll accept the argument that “First that human, over thousands of years, observing themselves and the animal world, and that concepts of engineering and control are derived from those observations,” with the proviso that you include that it was the observations of animals communicating via telegraphs and animals controlling telescopes that are the origins of modern scientific theories of communications and control in engineering.
But no, I only meant to imply only that the “origin of ideas” and “applications” are not coincident with the origin of scientific theories and investigations. No doubt every important idea in science has a pre-scientific origin. But what makes and idea scientific?--if you’ll allow, that seems to be the question you are asking.
But please continue to develop the notion of “interpretation,” as I find this a fascinating subject, related directly to the issue of semantics referred to above. I understand that the word originally had the sense of mediation. Usually I think in terms of shifts, transformations, or mappings. Is that helpful?
Also, I’m not so sure that understanding the point about “abstraction.” I’m not sure that “hardware” is any less “abstract” than “software.” Or that any of the words associated here or contraposed with “abstraction” are not themselves… abstract.
LOL RBH, Mesk, its “non-Darwinian” to the extent that Darwin would understand virtually nothing that you and the authors you cited are talking about! And I believe that Darwin was actually a pretty bright guy, in that monomaniacal way that some great scientists are. Why is it important that our ideas be “Darwinian”? It’s not the same in other sciences. No doubt all physicists recognize the singular genius of Newton, but they don’t insist that their theories be “Newtonian.” Geologists don’t insist that theories be “Lyellian.” I have two siblings who took the Hippocratic Oath, but I’m sure they would it amusing if I told them they must practice “Hippocratesian” medicine. Darwin should be allowed by biologists to be exactly what he was—a 19th century naturalist. Not a 21st century molecular biologist.
Also, just an aside about the “fuzziness” of analogical thinking. In engineering we seem to want to eliminate the fuzziness or exploit its richness. But it is often a very important issue in engineering that the formal identity of two systems be established—such as the identity of a model and the system it is a model of. (And biologists have the useful genetic notion of homology.) This would seem to be related to the ruminations about abstraction and material realization as well as the difference between analogies and identities. (I recall that it was also a subject that interested Kolmogorov, who provided some useful information-theoretic insights.) Would be interesting to explore the research on this subject.
Also, also (I just can’t shut up!): The shared notion “Life is technology” needs to be examined. If I have ever said that “Life is technology,” I should take it back. Life is like technology. But it is more like design. (And I do recall saying “Life is design.”) Design encompasses far more than technology.
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nobody
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posted 24. February 2003 14:15
charlie d. makes an important point I had been thinking about yesterday, but never had time to post:
quote:
Living organisms must receive, process and transmit information - that's in essence what life is all about. Organisms receive genetic information at their inception, must interpret it to develop/grow, and must transmit it to their progeny. Organisms also must receive and process information form their environment, and obviously do exchange information with other organisms and or within themselves. There is really no other way life as we know it can exist.
This agrees with the view of life as being high technology. Very high technology. Humans do not currently have the ability to match the technology of life and I doubt we could even create a robot that was smart enough to match all of charlie d.'s criteria. We do have some robots that are capable of some impressive things based on information they receive and process, but that requires excellent programming to achieve those results. And, as I think I've said before, excellent programming requires an excellent programmer.
Someone made the point, I think it was in this thread but I can't find it right now, that Darwin would not have understood this particular conversation. The programming of life would have would have made absolutely no sense to him because of the low technological level of his era.
Btw, I'm not a biologist but the term "programming of life" is already being used by people in the field. I just did a quick google and found this comment about the Human Genome Project:
http://www.gshh.uwa.edu.au/pastevents.html
quote:
Abstract
The Human Genome Project - Understanding Ourselves
The first phase of the Human Genome Project, the draft sequence of human DNA, was completed early in 2001, well ahead of schedule. The Human Genome Project is in fact the flagship for a fleet of projects covering bacteria, fungi, plants and animals, which are exploring the genetic programming of life and its diversity.
I think this term will gain more acceptance as more and more people study this area.
P.S. Sorry for the double post. I forgot to preview. I destroyed the quote the first time around. Hopefully the moderator can delete my first attempt. Thank you.
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charlie d.
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posted 24. February 2003 14:49
Keep your thumb-up to yourself, nobe. ![[Wink]](wink.gif)
Though I am glad you approve of my insight, my point was of course exactly the opposite as yours. Since life as we know it can't exist without processing and transmission of information, it is entirely unsurprising that biological systems work as information transmitters/receivers and processors.
On the other hand, if we could imagine hundreds of alternative ways to make information-free life, it would indeed be an intriguing coincidence that the underlying logic of the only life we knew about resembles information systems. As it stands, however, I don't see any reason to suspect that life's use of information is anything more than just a chemical/physical necessity.
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gedanken
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posted 24. February 2003 17:13
Can someone do what I requested earlier, and give a definition of "information"?
"Information" from Dictionary.com
- 1. Knowledge derived from study, experience, or instruction.
- 2. Knowledge of specific events or situations that has been gathered or received by communication; intelligence or news. See Synonyms at knowledge.
- 3. A collection of facts or data: statistical information.
- 4. The act of informing or the condition of being informed; communication of knowledge: Safety instructions are provided for the information of our passengers.
- 5. Computer Science. Processed, stored, or transmitted data.
- 6. A numerical measure of the uncertainty of an experimental outcome.
- 7. Law. A formal accusation of a crime made by a public officer rather than by grand jury indictment.
1,2,3,6, and 7 are inadequate for this thread. (Specifically 6, though used by Dembski, is not what is meant in biology because it applies equally to geology and thus does not meet the distinctions as discussed here.)
If it’s 5, that’s fine except that there is no “data” except as is exemplified in physical forms. In this case positions of rocks are “data” and thus “information”. It is a variation of what I proposed, but consistent in the sense that such physical properties of objects are “data” and thus there is no real distinction between physics and biology in this regard.
That leaves 4. But how is “knowledge” actually communicated in any biological system? (Except strictly in the nervous system, but I think that the meaning intended in this thread is that DNA and chemical ‘messenger’ processes, etc., are to be considered as communication and “information”.) So I think that the meaning, taken from this item, is reduced to issues of stimulus-response as the description of “communication” occurring (over a channel). I would like to see someone defend this meaning (especially in light of my previous posts). And if not defending this, please give a definition of "information!"
[ 24. February 2003, 17:35: Message edited by: gedanken ]
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charlie d.
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posted 24. February 2003 21:54
Gedanken:
Oh well, at risk of having all the info theorists here laugh me off the board, I'll give my own tentative definition, which looks a little bit like #5 but not exactly. I'd say that information is the interpretable representation of something in a different format (physical medium).
Thus, inanimate objects like a rock, or a snow flake indeed can contain some information (about their origin and "history", for instance); however, if I kick a rock from here to there, the information about the kick is not really stored in the rock in any interpretable format, and as such is not really information.
Biological organisms are unique in that they can detect information, store it, process it (change the medium in which its represented), elaborate it (eg, combine information from multiple sources), and retransmit it. Some of this is the inescapable nature of replicators; moreover, selection also necessarily imparts information on imperfect replicators in the form of differential reproduction. That's why I am saying that information detection, storage and transmission is a necessary mechanistic property of life.
[ 24. February 2003, 21:55: Message edited by: charlie d. ]
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gedanken
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posted 24. February 2003 23:09
Thanks, Charlie D,
quote:
Information is the interpretable representation of something in a different format (physical medium).
How soon does it have to be “interpreted”? (e.g. how far into the future, say is it still “information” in 300 years?) How likely does the “information” have to be interpreted -- e.g. can it have a chance of not being interpreted, is it information if there is a 5% chance it will be interpreted? What qualifies as a system that “interprets” information -- does a system that responds in some way “interpret”? What sort of way does the system have to respond in order to be “interpreting” the information?
(I don’t think that the strict “information theory” definition 6 would qualify, yet it might be used by the “information theorists”. So I think that this thread may need a slightly different definition than is used in some other locations. In fact I think that the different definitions are highly related and usefully interrelated. And there is a lot I like in Charlie D’s definition.)
PS, while you’re thinking about those questions, let me relate a little parable:
A man and a woman are talking over a telephone line. But there are extraneous noises on the telephone line, and the man is having difficulty getting the woman to understand. (Information is being corrupted by noise). Meanwhile a telephone technician is scanning the line with some technical equipment, trying to analyze from the character of the noise where the problem is occurring, because it has been an intermittent problem that is defying solution. So the technician is annoyed that the talking is corrupting his noise measurement, from which he will possibly interpret the point of source of the problem. But he knows that if they hang up the connection will be lost and so will the intermittent problem he has been searching for over the last month.
(By the way, I’ve actually done something very close to this. I had a customer who used an alternate telephone company that connected to the main tel co’s switches. But for calls from my area to that particular switch in that area, but only for that alternate telephone company’s customers, the main tel co routed the connection over an old trunk line with only one wire still in service. All the rest of the wires had been removed from service due to noise or other problems. We wound up being the guinea pig, and getting the alternate phone company technicians scanning the line when a problem occurred, and then keeping the connection open while they ran it down. The plot thickened when they figured it out, and the alternate telephone company was going to try to investigate whether the main tel co had been purposely creating problems for them. There was very significant amount of “information” in the nature of the technical problem.)
[ 24. February 2003, 23:54: Message edited by: gedanken ]
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gedanken
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posted 25. February 2003 00:21
Janitor@MIT said:
quote:
But no, I only meant to imply only that the “origin of ideas” and “applications” are not coincident with the origin of scientific theories and investigations. No doubt every important idea in science has a pre-scientific origin. But what makes and idea scientific?--if you’ll allow, that seems to be the question you are asking.
I wasn’t so interested in whether it was “scientific” at that juncture, as in distinction of the origin. Mike alluded to a possible origin of life’s character in the acts of an other intelligence, and prompted by the observation of similarity to communication processes that are created by our own intelligence. My point is that the intelligence itself, including the “communication processes” are due to the same natural processes, and that we learned (as I said and you apparently disagree) to create technical communication processes and theory from first observing natural systems including our own intelligence and communication (prior to “theory”).
quote:
Also, I’m not so sure that understanding the point about “abstraction.” I’m not sure that “hardware” is any less “abstract” than “software.” Or that any of the words associated here or contraposed with “abstraction” are not themselves… abstract.
Bingo! Then you do understand.
Several people (including the original Shapiro papers) were commenting on the “software” as distinct from the hardware. The question was not the origin of the hardware which is assumed to be somewhat understandable by natural evolutionary processes, but where does the software come from? That software and hardware is interchangeable and not really distinct (especially in systems like biological systems where all information is clearly stored in distinct biochemical formats) is precisely my point.
(Software is often viewed as an abstraction while hardware as the physical. This distinction is made because the software is more generalized than the hardware in a computer system, the hardware is constant while the software changes. Now this occurs as viewed in physical software as electrons stored in memory cells, and it occurs in abstractions of software as abstract state sequence definition even more abstracting than the abstraction of the idealized hardware on which it runs. The Turing Machine, abstract, can be viewed as the hardware, and the tape as data. But the tape, data, can be interpreted as software, and there are notions of compilers from one Turing Machine hardware to another, compiling the software held on the even more abstract and generalized tape. But anything that can be done in the software abstraction of a program on the TM tape, can be done as a hardware state machine definition of the TM itself. So ultimately there is no distinction between software and hardware, they are interchangeable, they are equally abstract after all. There is no difference in the question of where the software came from the question of where the hardware came from. The software does not change while the hardware stays the same, because the hardware changes concomitantly with the “software” in biological systems. Of course some hardware stays the same, but so does the “software” that patterns that constant hardware, so there is still no distinction.)
quote:
But I’ll accept the argument that “First that human, over thousands of years, observing themselves and the animal world, and that concepts of engineering and control are derived from those observations,” with the proviso that you include that it was the observations of animals communicating via telegraphs and animals controlling telescopes that are the origins of modern scientific theories of communications and control in engineering.
What was Bell doing when he accidentally invented the telephone? Answer: In one aspect, he was studying how sound could be translated to visual appearance. See (one) History of the Telephone:
quote:
Bell's father was a teacher of the deaf, and he imparted this knowledge to his only surviving son--Bell's brothers died of tuberculosis. Bell was the only telegraph inventor who understood how much we communicate via speech. He tried to build devices that would allow the deaf to see the pattern of speech sounds they were making and compare them with a kind of template. One of these devices was built around an actual human ear, which gave Bell an intimate understanding of how sounds are turned into waves by the bones of the middle ear.
These experiments led Bell to propose that the way to create a 'speaking telegraph' was to 'follow the analogy of nature'. Inventors often adopt this strategy: if nature has solved a problem, why not imitate nature? Bell, with help from his assistant Watson, built a kind of electromechanical ear in 1875, in which one spoke into a tube that ended in a membrane like the eardrum; a piece of metal was glued to the membrane and attached with a hinge to an electromagnet, which amplified the vibrations much like the bones of the middle ear [3]. This first telephone came about as a result of an accident. Watson had been trying to transmit telegraph signals; when one of the metal reeds got stuck, he plucked it in an effort to break it free. Bell came rushing into the room to find out what Watson was doing, because he had heard a strong signal in the other room from the receiving reed, strong enough so that he knew he could use this simple device to transmit speech. Like many other inventors, Bell took advantage of accidents and mistakes that would have been ignored by someone else.
As to control, we observe ourselves doing control first. That is the first observation of nature. (A baby recognizes faces, and makes demands by instinct and conditions, but the first observations in which there is considerable feedback is to move arms and watch where they go, learn to touch.) To try to do this in an extension to other mechanical means (other than the mechanical means of our own arms for example) is hardly a stretch. (Notice also a strong dose of the “Darwinian” survival of the accidental result kept because of its relevance to the work.)
Use all this as context when re-reading Wiener. Cybernetics was a return to this context of understanding nature in creating design, not of course the first step.
[ 25. February 2003, 01:36: Message edited by: gedanken ]
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Frances
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posted 25. February 2003 00:24
I personally like the definition given by Shannon which is btw the same as used by Dembski to define information. Basically information is the reduction in uncertainty. This definition does allow for a rigorous mathematical foundation to address the concept of information (biological). In fact using Shannon's concepts of information and the second law of thermodynamics I believe one can derive the lawof 'conservation' of CSI for closed systems and similarly show that for open systems (including systems with intelligent inputs) no such restrictions exist.
Shannon information can also be used to track evolutionary algorithms and their performance to 'transfer' information from the environment into the genome.
Schneider, Adami and others have begun to explore this interesting world of information as it applies to biology.
[ 25. February 2003, 16:21: Message edited by: Frances ]
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gedanken
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posted 25. February 2003 20:30
Frances suggests the “the reduction in uncertainty” definition, from Shannon. A reduction of uncertainty implies some measurement of uncertainty, and probability is the normal measure of uncertainty. Frances also mentions that Dembski uses this same definition.
For a moment, I would like to take a detour into the question of probability:
There are concepts of conditional probability, and its opposite, which I suppose might be called “unconditional” probability to distinguish it from conditional. Now conditional probability occurs when one speaks of additional conditions on the actions of the system, and examines the ways of outcomes in terms of ratios of occurrence or other probability measure when considering those additional constraints.
But is there any consideration of “probability” in which we are not naming constraints? Is there “unconditional” probability? I answer that there is not, that we are always considering conditions or constraints when we consider probability -- just that we may for a moment consider a universal set of conditions and then later additional conditional constraints on top of the original universal conditions. So “conditional” probability is completely valid designator and distinction from the lack of those additional conditions beyond the original problem conditions -- but no probability is without conditions or constraints.
Dembski says in Intelligent Design as a Theory of Information popular paper:
quote:
What then is information? The fundamental intuition underlying information is not, as is sometimes thought, the transmission of signals across a communication channel, but rather, the actualization of one possibility to the exclusion of others. As Fred Dretske (1981, p. 4) puts it, "Information theory identifies the amount of information associated with, or generated by, the occurrence of an event (or the realization of a state of affairs) with the reduction in uncertainty, the elimination of possibilities, represented by that event or state of affairs." To be sure, whenever signals are transmitted across a communication channel, one possibility is actualized to the exclusion of others, namely, the signal that was transmitted to the exclusion of those that weren't. But this is only a special case. Information in the first instance presupposes not some medium of communication, but contingency. Robert Stalnaker (1984, p. 85) makes this point clearly: "Content requires contingency. To learn something, to acquire information, is to rule out possibilities. To understand the information conveyed in a communication is to know what possibilities would be excluded by its truth." For there to be information, there must be a multiplicity of distinct possibilities any one of which might happen. When one of these possibilities does happen and the others are ruled out, information becomes actualized. Indeed, information in its most general sense can be defined as the actualization of one possibility to the exclusion of others (observe that this definition encompasses both syntactic and semantic information).
In discussing complexity and specificity he continues:
quote:
… First, let us show how to measure information. In measuring information it is not enough to count the number of possibilities that were excluded, and offer this number as the relevant measure of information. The problem is that a simple enumeration of excluded possibilities tells us nothing about how those possibilities were individuated in the first place. Consider, for instance, the following individuation of poker hands:
(i) A royal flush.
(ii) Everything else.
To learn that something other than a royal flush was dealt (i.e., possibility (ii)) is clearly to acquire less information than to learn that a royal flush was dealt (i.e., possibility (i)). Yet if our measure of information is simply an enumeration of excluded possibilities, the same numerical value must be assigned in both instances since in both instances a single possibility is excluded.
It follows, therefore, that how we measure information needs to be independent of whatever procedure we use to individuate the possibilities under consideration. And the way to do this is not simply to count possibilities, but to assign probabilities to these possibilities. For a thoroughly shuffled deck of cards, the probability of being dealt a royal flush (i.e., possibility (i)) is approximately .000002 whereas the probability of being dealt anything other than a royal flush (i.e., possibility (ii)) is approximately .999998.
…
(At this point Dembski goes on to describe the negative logarithm of probability (or negative entropy) measure to make information additive, but this is not relevant to my point.)
Now consider the poker hand, but with a twist: Start with a thoroughly shuffled deck of cards. Now I have a list before me of exactly the sequence of cards in the thoroughly shuffled deck, from the top. We deal the hand. How can I compute the probability of “A royal flush”? To do so, I would consider or write down the distribution of where the cards would be dealt, and if the royal flush occurred I would give that probability as unity, and if not I would list the probability as zero.
I bring up the twist because there are additional conditions implicit in the fair game of cards -- that I don’t know or don’t take into account such things as what physically happened in the shuffling or alternate sources of knowledge of how the random stack is shuffled. These are implicit conditions but they cannot be neglected. These are conditions of the problem specification for considering a probability.
The key point here is that in considering “a reduction in uncertainty” that one is considering probability of events from a certain set of constraints and from a certain viewpoint. Probability does not exist independent of the viewpoint or constraints of the problem. This set of constraints are indicative of how information or probability is interpreted.
End of detour.
More on Frances’s suggestion on using Shannon’s definition can be found in the PDF file An Overview of Information Theory from the Lucent site.
Some important aspects:
quote:
First, words are symbols to carry information between people. If one says to an American, “Let’s go!”, the command is immediately understood. But if we give the commands in Russian, “Pustim v xod!”, we only get a quizzical look. Russian is the wrong code for an American.
Second, all communication involves three steps – coding a message at its source, transmitting the message through a communications channel, and decoding the message at its destination.
In the first step, the message has to be put into some kind of symbolic representation – words, musical notes, icons, mathematical equations, or bits. When we write “Hello,” we encode a greeting. When we write a musical score, it’s the same thing – only we’re encoding sounds.
For any code to be useful it has to be transmitted to someone or, in a computer’s case, to something. Transmission can be by voice, a letter, a billboard, a telephone conversation, a radio or television broadcast, or the now ubiquitous e-mail. At the destination, someone or something has to receive the symbols, and then decode them by matching them against his or her own body of information to extract the data.
Fourth, there is a distinction between a communications channel’s designed symbol rate of so many bits per second and its actual information capacity. Shannon defines channel capacity as how many kilobits per second of user information can be transmitted over a noisy channel with as small an error rate as possible, which can be less than the channel’s “raw” symbol rate.
Shannon describes the elements of communications system theory as a source--encoder--channel--decoder--destination model. What his theory does is to replace each element in the model with a mathematical model that describes that element’s behavior within the system.
So here Shannon establishes a viewpoint (or more correctly the character of a communications and information viewpoint for purposes of the definition). And just like before, there is no “probability” independent of the constraints in consideration.
Once again we see clearly that information, according to Shannon’s information theory, is not independent of the question of the “information” being “interpreted”.
Now Dembski’s “information” is also subject to the issue of “interpretation” as I have demonstrated with the point that probability does not exist independent of this interpretation. As I showed, the actualization of possibilities, as observed depends on constraints of the problem and is thus not independent of interpretation of the event. Indeed there is no new information in the royal flush if we already knew the card order of the deck, it is the interpretation of the cards by the viewer with knowledge of what a royal flush is and furthermore assuming random deck that gives this interpretation “information”. And there are inconsistencies in Dembski’s use that form contradictions -- so what we do here cannot be consistent with all of Dembski’s use since they are self-contradictory. But that is a subject for another thread and cannot be explored here because it diverges too far from this subject.
Dembski suggests that the “channel” is not essential to information, rather actualization. But it is the interpretation of the actualization in the system being viewed (and according to the constraints of our model of that system) that allow approximations or calculations of probability. If multiple communication paths existed (e.g. the “channel” was not well-defined) then the situation model can be very different -- consider my example where someone knew (by independent channel) the sequence of cards being dealt. The “information” (as measured in a probability model) is very different if the separate communication channel exists when the cards are turned up, from the model where the only channel is considered randomness of the cards and the direct movement of cards to viewer as only “channel”. Dembski’s actualization is not independent of “channel”, nor is it independent of interpretation in the system in question. The meaning (existence) of a “royal flush” is an act of interpretation, and the probability model is a claim about the channel (card transfer) having a particular outcome (interpretation of royal flush) with a particular probability (from constraints of the model including the communication channel).
In addition, we are not considering (as our constraints of the problem) that we want the probability of a royal flush given the primordial state of the universe, we specify it in terms of starting with the shuffled cards or cards and process of shuffling without knowledge of how the shuffling will come out. Thus the start point of the “communication channel” can be identified as the starting event in the card hand. Similarly in all biological systems we have such identifications -- which are essential to identify any probability measures so as to quantify information.
(By the way, Dembski’s “explanatory filter” is really about the subject of these side channels of information communication. If the model of the primary pathway or “channel” is not consistent with observed results, but a model with an alternate pathway or “channel” is consistent, then the alternate channel can be considered as more reasonable explanation. Dembski claims in essence that the primary channel is inconsistent if the information model gives a probability of less than the UPB.)
This relates back to the biology question because in the biological system some subsystem must “interpret” the symbols delivered in some delivery pathway “channel”.
So we have two definitions of information so far:
Charlie D: Information is the interpretable representation of something in a different format (physical medium).
Frances: Information is the reduction in uncertainty.
These definitions are not inconsistent at all. Charlie D’s definition does not include the quantification based on probability. And Frances’s definition leaves to ellipsis the issue of “interpretation”, but that issue is part of the definition anyway and can be made explicit.
[ 25. February 2003, 21:47: Message edited by: gedanken ]
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nobody
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posted 25. February 2003 21:59
Dictionary.com gives several definitions for information. This one applies:
"Computer Science. Processed, stored, or transmitted data."
This definition agrees with charlie d.'s previously posted description of life. Quote: "Living organisms must receive, process and transmit information - that's in essence what life is all about."
This also agrees with Mike Gene's observation about biology moving away from geology and towards high technology.
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gedanken
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posted 28. February 2003 01:45
I was thinking of starting to wrap up with some concluding remarks relating “interpretation” issue back to my prior topic of the terminology of communication just applying in a matter of degree. Charlie D’s definition was in terms of “interpretation”. And the standard Shannon definition has “interpretation” by a human or derivative almost specified -- though in the descriptive part and not in the short wording of the definition.
But what got me thinking was the aspect of Charlie D’s “representation of something in a different format”. This goes beyond “interpretation” (but may work hand in hand).
I was wondering how “different format” was meaningful in actual examples from biology? How is a messenger chemical process sending something symbolic or in a “different format”, and what does this mean in that context? And in things like DNA or genetic “information”, once again how are we interpreting the “in a different format” issue? (Especially since the DNA is directly part of the physical event sequence in a highly integrated physical manner.) Would someone with a biology background be willing to discuss this further?
Nobody,
If you’ll look back up the page, I did refer to the 7 Dictionary.com definitions, and made points about several.
But if we take “Processed, stored, or transmitted data” as the meaning, how do we deal with the following:
Consider a noise process that simply records computer data from that noise. (A possible example is an analog to digital converter, but the analog signal is just a white noise source.) This forms something that would be “computer data”, and it could be processed. But I am not sure that it captures any of the quality of “information” that I think we want to capture as aspects of biological systems. This gets back to my very questions just above. The discussion here has largely been in terms of “information” being communicated within some process that defines or controls a developmental process. I don’t see the “data” definition as capturing that at all -- and that is why I introduced my entire concept back many posts by partially defining “information” as distinct from “data” when it is “interpreted”. But there may be other ways to get at the issue. Any comments?
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nobody
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posted 28. February 2003 16:52
quote:
that is why I introduced my entire concept back many posts by partially defining “information” as distinct from “data” when it is “interpreted”. But there may be other ways to get at the issue. Any comments?
To address your use of the word "interpreted", maybe this brief information from the U.S. Department of Energy's Joint Genome Institute and the Lawrence Berkeley National Laboratory will be helpful. They say:
"Now that the sequence of the human genome has almost been completed the next challenge will be the development of a vocabulary to read and interpret that sequence," says Edward Rubin, M.D., director of the Joint Genome Institute (JGI) for the U.S. Department of Energy, and Berkeley Lab's Genomics Division"
That statement sounds very similar to someone who is attempting to back engineer software, in this case the software of life. You will also notice, when you go to the article, that they use the following phrase in the first paragraph:
quote:
biological information encoded in the human genome
There does not appear to be any question in the scientific community about the massive amounts of information contained within our DNA. Attempting to break the programming code is the next big challenge for scientists.
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gedanken
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posted 28. February 2003 17:48
Nobody, you took advantage of my question to make a point, but did not answer the question itself.
(The "interpretation" here was clearly by humans.)
Since you did not modify your definition in any way, it still does not indicate that any interpretation is needed for something to be "information". It can simply be stored and processed. To me that means that any arbitrary storage and any arbitrary "processing" is possible.
Earlier I was claiming that rocks moving in space contained "information" in their motion, with the "data" in the form of motion and energy. And that in essence an impact was a primitive "communication" of this information (and since it obeys certain 'algorithmic' constraints, the "data" was thereby 'processed' in an extremely simplistic manner.)
But I was trying to get more fully at the notion of information. I didn't want my point to be so easy. Although I feel that any level of processing of "data" can qualify as interpretation, I thought that there could at least be some differentiation of degree wherein some kinds of receiving are "interpretation" in greater degree than others.
To look at your poin in another way, biologists look at the processes of biology themselves as making some use of "information". In the way this was described, the genetic code only became "information" when it was interpreted by the human as "information". So this leads to another question:
Is it true that messaging systems withing biology are not true information and that such things as genetic code only become "information" when they are interpreted by humans? (If so there is information in a rock heading down a hill toward me when I interpret that, is there not?) I would be happy with such a definition, as it supports my primary point, but I don't think it gets at what others have meant by "information" in biology.
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Moderator
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posted 28. February 2003 21:10
Mike,
I'm going to leave this thread open for another day or two in case you'd like to say a few last words in summary. However, it seems to be getting off topic and I will probably close it down in a day or two.
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