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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 10. February 2003 23:54
James Shapiro's paper, Genome Organization and Reorganization in Evolution: Formatting for Computation and Function is a very interesting read.
He begins by noting that biology is undergoing a conceptual shift. He outlines some of these changes (for example, genetics is changing from a focus on genes as units of inheritance and function to a focus on genomes as interactive information systems) and notes developing themes:
quote:
There is a fine irony in the conceptual changes summarized in Table 1. The expectation of its pioneers was that molecular biology would confirm the reductionist, mechanical view of life.1—3 However, the actual result of molecular studies of heredity, cell biology and multicellular development has been to reveal a realm of sensitivity, communication, computation and indescribable complexity.4—6 This year’s Nobel Prize in Medicine illustrates this point: the recipients were recognized for identifying components of the molecular computational network that regulates the eukaryotic cell cycle.7 Special mention was made of the concept of checkpoints, the inherently computational idea that cells monitor their own internal processes and make decisions about whether to proceed with the various steps in cell division based on the information detected by surveillance networks.
This point goes back to something Paul Davies noted, as he appraoched the topic of biology from the perspective of a physicist:
Concepts like information and software do not come from the natural sciences at all, but from communication theory, and involve qualities like context and mode of description - notions that are quite alien to the physicist’s description of the world. Yet most scientists accept that informational concepts do legitimately apply to biological systems, and they cheerfully treat semantic information as if it were a natural quantity like energy. Unfortunately, “meaning” sounds perilously close to purpose, an utterly taboo subject in biology. So we are left with the contradiction that we need to apply concepts derived from purposeful human activities (communication, meaning, context, semantics) to biological processes that certainly appear purposeful, but are in fact not (or are not supposed to be).
It is striking to me that to truly understand the essence of life and to describe the basic workings of life, a strongly teleological viewpoint not only remains, but leads the way. That is, to understand cell cycles, we really need to think in terms of "communication theory." Cell division is smart technology.
And this leads to Shapiro's second major theme:
quote:
In addition to uncovering intra- and inter-cellular computing systems (frequently referred to as "signal transduction" networks), molecular analysis has also confirmed the generality of Barbara McClintock’s revolutionary discoveries of internal systems for genome repair and genome restructuring.8 The ability of all living cells to take action to conserve or change their DNA sequence information was unknown when the basic concepts of Mendelian genetics were formulated. In that period of ignorance, it was assumed that genomes are constant and only change by accident. The discovery of repair systems, mutator functions and mobile genetic elements (MGEs) brought the phenomena of mutation out of the realm of stochastic processes and into the realm of cellular biochemistry.9-15 DNA biochemistry is not fundamentally different from the biochemistry of metabolism or morphogenesis. Consequently, our notions about the evolutionary sources of genomic differences that underlie biological diversity and adaptive specialization require a profound re-evaluation. All aspects of cellular biochemistry are subject to computational regulation. So we can no longer make the simplifying assumption of randomness, and we have to incorporate the potential for biological specificity and feedback into evolutionary thinking.
It naturally follows that smart cells might evolve smartly. That is, they are not helpless victims of circumstance and environmental changes, but exert themselves actively. The dynamic genome can be viewed as a form of technology that makes intelligent use of natural selection.
Shapiro again draws heavily from teleological metaphors:
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Applying the computer storage system metaphor, the ideas summarized in Tables 2 and 3 can be restated by saying that the genome is formatted for interaction with cellular complexes that operate to replicate, transmit, read, package and reorganize DNA sequence information. Genome formatting is similar to the formatting of computer programs in that a variety of generic signals are assigned to identify files independently of their unique data content. We know that different computer systems employ different signals and architectures to retrieve data and execute programs. In an analogous fashion, diverse taxonomic groups often employ characteristic DNA sequences and chromosomal structures to organize coding information and to format their genomes for expression and transmission. Thus, one of the consequences of evolutionary diversification is the elaboration of distinct Genome System Architectures.20
I'll take a closer look at Shapiro's example of the lac operon in the next night or so.
[ 10. February 2003, 23:55: Message edited by: Mike Gene ]
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Frances
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posted 11. February 2003 12:57
While teleological metaphors may be helpful describing these fascinating details of how life evolves we should be careful to intepret them truely as "goal driven", unless of course the goal is survival.
For instance what was initially thought to be adaptive mutations now seems to be a hypermutation response of the organism.
Terms such as genetic toolbox, control, feedback etc all have been succesfully applied in our own world of technology, reapplying much of what nature had already found. Shapiro has some very interesting papers and presentations on these issues that I encourage all to read. If intelligent design in nature were to refer to the processes through which organisms 'manipulate' their chances of survival then I do not believe that we have much disagreement. But is this really the form of ID that seems to appeal so much to Behe and Dembski et al? Is intelligent design inclusive of natural processes as the designer?
Fascinating ideas.
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posted 11. February 2003 13:11
Frances,
Where does Mike Gene even imply what you ask in the following:
quote:
But is this really the form of ID that seems to appeal so much to Behe and Dembski et al?
Can one not just be impressed with the work of another scholar, the angle from which he is attending his work, without immediately lumping his work into "the form of ID that seems to appeal so much to Behe and Dembski."
Is Mike Gene even implying this?
Your continued persistence in trying to frame every discussion around a narrow form of intelligent design, along with the fact that you have once again violated board rules (e.g. don't make a first post), you are receiving another day long ban. It is the last day long ban and will be followed by a week if you don't start cooperating.
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Erik
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posted 12. February 2003 14:59
quote:
Mike Gene (quoting Paul Davies): Concepts like information and software do not come from the natural sciences at all, but from communication theory, and involve qualities like context and mode of description - notions that are quite alien to the physicist’s description of the world. Yet most scientists accept that informational concepts do legitimately apply to biological systems, and they cheerfully treat semantic information as if it were a natural quantity like energy. Unfortunately, “meaning” sounds perilously close to purpose, an utterly taboo subject in biology. So we are left with the contradiction that we need to apply concepts derived from purposeful human activities (communication, meaning, context, semantics) to biological processes that certainly appear purposeful, but are in fact not (or are not supposed to be).
My guess is that the quote comes from the book "The Fifth Miracle", but I'll need the page number to check it (besides, a quote containing stuff used for argumentative purposes should never be reproduced without a full reference to the source from which it was copied). Davies's descriptions of these things in his book "The Fifth Miracle" is not always good, so it may not make sense even within its larger context, but I may want to (re)read it the next time I visit the library.
quote:
Mike Gene: It is striking to me that to truly understand the essence of life and to describe the basic workings of life, a strongly teleological viewpoint not only remains, but leads the way. That is, to understand cell cycles, we really need to think in terms of "communication theory." Cell division is smart technology.
Communication theory has very little to with semantic meaning (in the sense that no considerations of semantic meaning is made in communication theory--of course, anyone is free to try to formulate a theory of semantic meaning that uses stuff from communication theory, but communication theory can stand alone without such a theory). Rather, it is about how to transmit data so that (i) what is sent by the sender is the same as what is received by the receiver, and (ii) the transmission is efficient. Just as mailmen and the postal service are expected to deliver letters regardless of whether they make sense or not, a communication enginner is typically expected to build data encoders, transmission channels, and decoders that deliver to the receiver what the sender actually sent without considerations of semantic meaning. A typical communication channel should work for transmitting English texts, for transmitting images, for transmitting randomly generated numbers, etc. Think of your telephone, which allows you to transmit audio data to someone else regardless of whether or not you are saying something interesting. That the channel may be used for faithful transmission of nonsense is simply not the communication enginneer's problem.
Therefore you need to elaborate how thinking in terms of communication theory amounts to a strongly teleological viewpoint.
Erik
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Michael M. Halassa
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posted 12. February 2003 15:43
I haven't read this paper in particular, but I have read other work by Shapiro. Adaptive evolution is a neat concept, and it does change our understanding of mutations from being random into being a part of a systematic biochemical circuit.
I just wonder how signifcant this process will be at the level of a multicellular organism. I mean, if this happens in the germ cells of a multicellular organism who is undergoing a particular challenge then it might offer protection to its progeny. However, there should be various groups of genes that will be able to sense the environment and induce the particular changes in the relevant genes. This sounds like Lamarkism, and I do not know if there has been any experimental evidence to support such genes in animals, or theories of how specifically they might function. On the other hand, if those processes happen in somatic cells, I would suspect very little chances of benefit for the organism. It is hard to imagine how these processes would be able to induce the same change in genes across numerous cells. Unless there is, again, a proposed mechanism for how they might work.
I would be grateful for any response on this matter.
Michael
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Nel
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posted 13. February 2003 23:23
Erik,
Standard communication theory does distinguish "meaning" from the amount of information it studies, but this is an irrelevant point.Communication theory, in and of itself as a is an expression of certain ways of representing variables and signals Mike was pointing to it's useful application to things like cell division. Here we have a design methodology used to understand biology. As Shapiro explains:
quote:
By ensuring that each daughter cell receives one and only one homologue copy of each duplicated chromosome, this is a highly non-random process. (If n chromosomes duplicated and then segregated into daughter cells randomly, the chance of each daughter receiving a full complement would be 2-n.) Equal distribution is guaranteed by a checkpoint system delaying the active phase of cell separation (cytokinesis) until the duplicated and paired homologues are aligned along the metaphase plate and attached by microtubules to opposite spindle poles. Proper alignment and spindle pole attachment then lead to distribution of one homologue to each daughter cell at cytokinesis. Chromosome pairs that are not properly aligned and attached emit chemical signals. These signals are interpreted by the cell cycle control network and the homologue separation machinery as "WAIT" messages. In this way, the dynamic process of microtubules searching to attach onto unbound homologues is allowed to continue to completion. Only then, when every chromosome pair experiences the appropriate mechanical tension, does the inhibitory signal disappear and the cell make the decision to begin the series of events that separate the chromosomes and form two daughter cells.
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Mike Gene
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posted 14. February 2003 19:47
Nelson: Communication theory, in and of itself as a is an expression of certain ways of representing variables and signals Mike was pointing to it's useful application to things like cell division.
Indeed. And it's not just useful for cell division, but extends to all life forms and at various levels. Shapiro uses the lac operon as a nice illustration. So let's take a look:
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The computation-enabling aspects of lac operon organization become apparent when we understand how the various regulatory sites connect this locus to physiological data about glucose and lactose metabolism. The cell senses the presence of glucose indirectly by means of its uptake system.29 When glucose is available, a membrane-associated protein involved in transporting the sugar into the cell continually transfers phosphate groups to the sugar molecule, which enters the cell in a phosphorylated form. The transport protein itself thus exists almost all the time in the unphosphorylated form. When glucose is no longer available, this protein has no acceptor for its phosphate groups and so exists continuously in the phosphorylated form.
Thus, the cell takes an extracellular state [Glucose Present] and converts it into a cellular signal [Transport Protein Without Phosphate]. Of course, the inverse then holds true - Glucose Absent -> Transport Protein With Phosphate. The trick now is to amplify this signal:
quote:
When phosphorylated, it acquires the ability to activate the enzyme adenylate cyclase, which converts ATP into cAMP, thus raising the intracellular concentration of cAMP. The cell uses the phosphorylated transport protein and a high cAMP concentration as indicators that glucose is not available.
Thus, the extracellular state [Glucose Absent] is now converted into a strong cellular signal -> high concentrations of cAMP. The cell's internal physiology has now changed to reflect the environment, but in a rather conventional manner - cAMP levels reflect the levels of extracellular glucose, but the two molecules are chemically unrelated. It is the logic of cell biology/physiology that relates the two. Yet cAMP by itself does nothing. It acts now as an amplified signal on another "receiver":
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The cAMP concentration is read by the CRP protein which binds to the CRP site in lac only in the presence of abundant cAMP. The presence of the cAMP-CRP complex bound to lac DNA stabilizes the contacts between lacP and RNA polymerase and so informs the transcription apparatus that the lac operon is ready for transcription.
Thus, the dynamic state of the genome is now altered and is poised to begin synthesizing the genetic information needed to compensate for an environment lacking the main fuel source (glucose). But at this point, we're only half-way there. When glucose is present, the cAMP signal is dampened and promoters for genes needed to metabolize other sugars are taken off-line. And this is a global control mechanism, as several metabolic operons are modulated this way, including those that would metabolize arabinose, galactose, maltose, in addition to lactose. Once the promoters are "powered-up" through the cAMP signal, it's now a question of which one gets brought on-line. Again, the cellular signal will have be coupled to detection of the environmental state:
quote:
In the absence of lactose, however, only rare transcription events can occur because LacI repressor molecules bind to two of the operator sites and create a loop in the DNA, blocking access to the lacP promoter. The cell also senses the presence of lactose indirectly. Low levels of LacY permease transport a few lactose molecules into the cell, where LacZ beta-galactosidase converts some of them to a related sugar called allolactose. Allolactose can bind to LacI repressor, induce a change in shape that makes the repressor unable to bind lacO, and so free lacP for transcription.
And this is the classic lac operon story. But Shapiro's take is most interesting:
quote:
Each of these molecular interactions constitutes an information transfer event, or logical statement, and the combination of all of them allows the bacterial cell to compute the algorithm enabling discrimination between the two sugars: "TRANSCRIBE lacZYA IF AND ONLY IF GLUCOSE IS NOT PRESENT, LACTOSE IS PRESENT, AND THE CELL CAN SYNTHESIZE FUNCTIONAL PERMEASE AND BETA-GALACTOSIDASE". 26
Yes, these are information transfer events. Certainly, we can focus on the chemistry, where a protein loses its substrate and thus remains phosphorylated and thus activates an enzyme that then generates its product which in turn binds to a protein that in turn binds to DNA and now stimulates RNA polymerase. But if we step back, we can appreciate this as a computation device whose chemical relationships are driven by the logic of the cell's organization. Shapiro puts it nicely:
quote:
Two features of the lac operon regulatory computation are particularly noteworthy and generalizable. (1) Information transfer occurs by the use of chemical symbols to represent empirical data about the physiological environment: cAMP, allolactose and protein phosphorylation levels represent the availability of glucose and lactose.
I like that - chemical symbols to represent empirical data about the physiological environment
And
quote:
(2) The regulatory network integrates many different aspects of cell activity (transport, cytoplasmic enzymology and energy metabolism) into the transcriptional decision. In other words, it is literally impossible to separate physiology from genomic regulation in E. coli — and, indeed, in any living cells.5, 6
Indeed. And this simple bacterial computation process foreshadows, shall we say, the manner in which metazoan development occurs. In fact, the similarities between the way E. coli computes its environment and the way your brain cells work to process these letters is strikingly similar. In other words, human learning will also make use of phosphorylation signals, cAMP signals, etc., that can feed into transcription and much more.
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nobody
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posted 14. February 2003 19:51
Thanks for the fascinating quotes Mike. (My computer is acting up right now, so I hope this post makes it through intact.)
You've reminded me of what the U.S. Dept of Energy says on their Genomes To Life page:
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Beyond the DNA Sequences
The plan for the 10-year program is to use DNA sequences from microbes and higher organisms, including humans, as starting points for systematically tackling questions about the essential processes of living systems. Advanced technological and computational resources will help to identify and understand the underlying mechanisms that enable organisms to develop, survive, carry out their normal functions, and reproduce under myriad environmental conditions.
The Human Genome Project did not provide all the answers that some scientists had hoped for. Instead it opened a lot of eyes to the incredible programming of life. Programming that we humans cannot match. Programming that we humans cannot even fully understand at this time.
Programming, even when it's programming that is created by only using chemicals, requires a programmer. A highly intelligent programmer.
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Mike Gene
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posted 14. February 2003 20:53
Frances: But is this really the form of ID that seems to appeal so much to Behe and Dembski et al?
When you consider the description of the lac operon, there are clearly echoes of IC and CSI. While they probably don't echo strongly enough to support the "it couldn't evolve" position, I think they might be suggestive of a position where it makes more sense to view life as technology rather than the emergent properties of geology. The fact that biology not only depends on teleological metaphors, but actually needs them to shed real light on biology, doesn't exactly weaken this claim. Nevertheless, I have always made my interests clear - this is a provisional investigation that must remain open-ended, sensitive to subtle clues, and doesn't demand sensational/extraordinary evidence.
Is intelligent design inclusive of natural processes as the designer?
Interesting question. A designer may very well have designed life with the ability to design. That's why I noted that life makes intelligent use of natural selection. From a purely non-teleological perspective, natural selection relies on coincidence. But a teleological perspective allows us to begin viewing natural selection as something that is being smartly used. Consider Shapiro's thesis of a natural genetic engineering toolkit. This is an incredibly intelligent way to exploit natural selection. Take the CAP binding sites. The mechanisms outlined in Table 4 of Shapiro's article are a much smarter way of distributing these than waiting for such binding sites to randomly mutate into existence in the proper place.
The reason our crude technology can create transgenic animals is simply because we have learned how to piggy-back on the sophisticated life processes.
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Mike Gene
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posted 14. February 2003 20:58
Nobody: You've reminded me of what the U.S. Dept of Energy says on their Genomes To Life page
There's a certain logic to needing technology to unlock technology. ![[Smile]](smile.gif)
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Mike Gene
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posted 14. February 2003 21:09
Here's some excerpts that supplements Shapiro's thesis:
Life as Communication
by Arnold De Loof
Posted December 10, 1999 · HMS Beagle Issue 68
Life has many different meanings, as outlined in any dictionary. It is not possible to find one universal definition covering all meanings. The best one can hope for is to find a common denominator for all these different meanings. In my view, what biologists call "life" is simply communication activity exerted by a communicating compartment (system).
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According to this approach, life is not a state and not a machine, but the activity of a machine. This definition automatically implies that life uses both hardware and software. The continuation of life requires a double continuum: that of its hardware and that of the software (needed to decode the incoming messages).
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This view of life has profound consequences for the theory of evolution. Neo-Darwinism explains only the evolution of the instruments of communication - the hardware. At least as important is the evolution of the software. But this type of evolution is not governed by the laws of genetics, but by those of communication. By logical deduction, the conclusion can be reached that the driving force of evolution is not selection, but communication activity (that is, life itself). Selection is not a cause, but is itself a result of something that happened before. When I made this deduction a few years ago, I could not believe it myself - but there is no way around it.
The complete article is here.
[ 14. February 2003, 21:10: Message edited by: Mike Gene ]
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Mike Gene
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posted 14. February 2003 21:16
De Loof: Neo-Darwinism explains only the evolution of the instruments of communication - the hardware. At least as important is the evolution of the software.
And this relate to something that Barrow and Tipler explained in their book, The Anthropic Principle (which has also been echoed by Dembski and Davies):
quote:
The limitation of explanation in terms of mechanical causality can perhaps be best understood by comparing a living being to a computer. As Michael Polanyi has pointed out the internal workings of the computer can of course be completely understood in terms of physical laws. What cannot be so explained is the computer's program. To explain the program requires reference to the purpose of the program, that is, to teleology. Even the evolution of a deterministic Universe cannot be completely understood in terms of the differential equations which govern evolution. The boundary conditions of the differential equations must also be specified. These boundary conditions are not determined by the laws of physics which are differential equations...The universal boundary conditions are as fundamental as the physical laws themselves; they must be included in any explanation on par with the physical laws."
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Mike Gene
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posted 14. February 2003 21:29
Sorry for the multiple postings, but I don't get a chance to post during the week:
Here's another interesting excerpt from Shapiro:
quote:
What significance does an emerging interface between biology and information science hold for thinking about evolution? It opens up the possibility of addressing scientifically rather than ideologically the central issue so hotly contested by fundamentalists on both sides of the Creationist-Darwinist debate: Is there any guiding intelligence at work in the origin of species displaying exquisite adaptations that range from lambda prophage repression and the Krebs cycle through the mitotic apparatus and the eye to the immune system, mimicry, and social organization? Borrowing concepts from information science, new schools of evolutionists can begin to rephrase virtually intractable global questions in terms amenable to computer modelling and experimentation. We can speculate what some of these more manageable questions might be: How can molecular control circuits be combined to direct the expression of novel traits? Do genomes display characteristic system architectures that allow us to predict phenotypic consequences when we rearrange DNA sequence components? Do signal transduction networks contribute functional information as they regulate the action of natural genetic engineering hardware?
Questions like those above will certainly prove to be naive because we are just on the threshold of a new way of thinking about living organisms and their variations. Nonetheless, these questions serve to illustrate the potential for addressing the deep issues of evolution from a radically different scientific perspective. Novel ways of looking at longstanding problems have historically been the chief motors of scientific progress. However, the potential for new science is hard to find in the Creationist-Darwinist debate. Both sides appear to have a common interest in presenting a static view of the scientific enterprise. This is to be expected from the Creationists, who naturally refuse to recognize science's remarkable record of making more and more seemingly miraculous aspects of our world comprehensible to our understanding and accessible to our technology. But the neo-Darwinian advocates claim to be scientists, and we can legitimately expect of them a more open spirit of inquiry. Instead, they assume a defensive posture of outraged orthodoxy and assert an unassailable claim to truth, which only serves to validate the Creationists' criticism that Darwinism has become more of a faith than a science.
[ 14. February 2003, 21:30: Message edited by: Mike Gene ]
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gedanken
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posted 14. February 2003 21:52
In the thread algorithmic info, probability, etc. (including successive posts) I make the point that an arbitrary amount of the “software” of a Turing machine with a “program” (software) on tape can be transferred to the actual state machine representation of the Turing machine. Thus certain measures like Kolmogorov complexity are subject to certain viewpoint issues. (Also see my first post which is in more descriptive terms rather than highly technical terms of the thread.)
The point of relevance to this thread is that the “software” in biological systems, somewhat analogous to my example of transferring from the tape to the Turing state machine, exists in the physical and analog state and is not an abstraction. Forms of so-called biological information, like genetic code, exist as actual physical molecules. And my analogy to the Turing machine state machine is not to consider the abstract state machine, rather to note that the software could be in software form (on tape media and thus subject to greater abstraction) in a Turing Machine, or it could exist in the hardware state processing that implements the Turing machine. I will argue that the so-called “software,” and other types of “information” in biological systems are all implemented in the hardware aspect and do not exist as abstractions. The abstractions (including analogies to “software” and other types of “information”) are created by scientists in describing these systems.
Real computers (as opposed to abstract state representations like Turing machines or conceptual “algorithms”) work as real physical systems. Bits are actually analog states of matter in the physical subsystems of memory and electronic register cells, either stored as charge or as current flow or some (possibly dynamically changing) combination. Real computers do not, for example, produce deterministic results -- no matter how much their designers attempt to achieve that goal.
Biological systems likewise have their so-called “software” or information stored in physical forms, like in the physical molecules of genetic material.
In another thread I was pointing out how algorithms are used even in computing the information that is contained in the pathways of the planets and their images as they appear on Earth. But these computations (algorithms) are abstractions, what we learn is to make abstract models of these physical systems. Our abstract models are not the systems themselves, rather they are creative attempts to understand physical reality.
We mimic nature and learn from nature in order to create our models of reality.
An aspect that these posts of this thread seem to point out, is how the “information” in biology is in a state of communication -- just as is used in information theory in the subject communication design. This is very distinct from the character of other attempts to measure “information” as some absolute quantity, rather than as a relative quantity relative to the abstraction of the functional form of point-to-point transfers in the system in question. I see these posts as being very valuable in understanding the transitive nature of the communication of “information” in biological systems, similar to the transitive nature of information as observed in many other parts of nature, measured in terms of point-to-point transfer processes.
Because the entirety of the subject of communications theory development of terms like “information” is to deal with the problems of communications in real physical media. Real physical media (unlike idealized abstractions thereof) have real errors and do not operate in a wholely consistent manner. Thus the “information” theory is relevant to transfers from point to point, and information is defined relative to that notion. But such information theory is actually applicable to almost any physical process -- even an asteroid hitting a moon can be viewed as imparting “information” from the standpoint of communication theory. The reason information views are important in biology are because of the high degree of complexity in the cause and effect relationships, and thus are more useful than simpler cases of cause/effect relations.
In other fora I have highly recommended Norbert Wiener's Cybernetics: or Control and Communication in the Animal and the Machine. (And also The Human use of Human Beings: Cybernetics and Society.) These books show how we have abstracted much of the concepts of information and control system from our observations of nature -- as opposed to the other way around.
[ 15. February 2003, 00:59: Message edited by: gedanken ]
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posted 14. February 2003 22:45
Nobody,
Please do not post at Brainstorms if all you're doing is cheerleading, and that is what it sounds like you are doing in your above post. We prefer posters who propose creative ideas, not those who seem to be involved in a victory chant.
Thanks.
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