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Topic: Shapiro on the Genome
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nobody
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posted 15. February 2003 04:11
Mike Gene says:
quote:
There's a certain logic to needing technology to unlock technology.
Yes. It's completely logical. It's known as reverse engineering. Our military does it with weapons from other countries. However, it often takes a lot of intelligence and a lot of advanced technology to reverse engineer. It's usually not an easy task.
On the other hand, a stone age culture, no matter how intelligent they might be, could never reverse engineer a jet because they do not have the required technological base.
A world leader in technology is IBM. I find it extremely interesting that they are attempting to reverse engineer some systems in living things. Here's a relevant quote from a section of one paragraph, including a short comment relating to your comment about cell division:
"Reverse engineering metabolic and gene regulatory networks
An understanding of the behavior of biological systems at each level of their organization can only be achieved by careful study of the complex dynamical interactions between the components of these systems. For this understanding to be quantitative it is necessary to develop structurally, biochemically and biophysically detailed mathematical models. Two systems under study by our group and others are metabolic and gene regulatory networks. Metabolic pathways have been study for many years, and the basic components are understood in many organisms (for example, see KEGG, the Kyoto Encyclopedia of Genes and Genomes). However, the current picture is of metabolic pathways is essentially static, a diagram on a page. In contrast, real cell are dynamic with metabolisms that can react to an ever-changing environment. These mechanisms are designed to keep some level of homeostatsis in the cell but also to allow for dynamic responses under appropriate conditions (i.e. protein synthesis is elevated before cell division). Therefore, a true understanding of metabolism will requires knowledge of both dynamic and homeostatic mechanisms, plus an understanding of the governing intra- and extracellular regulatory systems. Clearly, this is immense problem, and the complete cellular data to construct such models does not exist at current. We developing algorithms to reverse engineer cellular metabolism by making best use of the incomplete data sets currently at our disposal."
http://www.research.ibm.com/FunGen/
That says a whole lot. IBM could reverse engineer any computer system devised by humans, imo. However, even they address the fact that reverse engineering aspects of life is an "immense problem". Clearly we need more information.
The question is, even if we had all the necessary information, whether we have the required level of technology yet. Since you have previously stated, at ARN I believe it was, that even a minor reverse engineering project like building a flagellum from scratch is beyond current human technology, I think it is only fair to conclude that we cannot reverse engineer something like a gene regulatory network at this time.
The comparison of human programming with the chemical programming of life is clear. It's also clear that the technology of life is still far more advanced than current human technology. Prior to humans having computers, any chance of reverse engineering life was zero. Now, with the help of IBM and other advanced technology companies, we might be able reverse engineer some of the systems of life. I'm looking forward to any progress they might make.
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Mike Gene
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posted 15. February 2003 14:16
Nobody: On the other hand, a stone age culture, no matter how intelligent they might be, could never reverse engineer a jet because they do not have the required technological base.
I think that is an important point. If life was designed, it is reasonable to assume that the design is advanced beyond our current capabilities. Think what this means in terms of the history of science. Our ability to recognize life as designed would be dependent upon our technological development. And it's not simply a question of developing the technology needed to process the information needed to understand life. It's the weird way in which our technology parallels, thus illuminates, life processes meaning we can learn about the latter by appreciating the former.
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gedanken
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posted 15. February 2003 14:34
With regard to the IBM "reverse engineering", take a look at my comments on the previous page. They seem relevant, and were made with no knowledge that this variation of the subject would come up.
[ 15. February 2003, 14:36: Message edited by: gedanken ]
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kyle7
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posted 15. February 2003 20:33
Some interesting discussion.
I think the future of technology will be at the nano level as we mimic life. Biotechnology will become the primary focus as we engineer life-forms to manufacture cars, computers etc. Over time we may be able to master protein folding allowing a whole new world of engineering to emerge.
The desire to travel to other solar systems will also force us to the nano level. The only real feasible way for interstellar exploration will be to send nano-probes (or larger MEMs probes)containing genomic information or whole cells. The reason for going "nano" is that the energy required in accelerating mass to close the speed of light is extremely high:
K.E. = (mc^2)*[(1 - (u/c)^2)^(-.5) - 1]
where
K.E is the kinetic energy,
m is the mass,
c is the speed of light
u is the speed of the probe.
The reason for traveling near the speed of light is the distance to the nearest star -- over 4 light years away. The one factor that we do control is the mass, thus the need for nano spaceprobes. Engineers will design dynamic genomic systems that will use matter at other solar systems to assemble complex systems used to study the surrounding planets and send images and information back to earth. Possible, we will use "terra forming" to produce productive new planets ready to support human explorers sent from earth.
When we attain this level of technology, I think the notion of ID will gain momentum as we begin to discover the complexity of life.
[ 15. February 2003, 20:48: Message edited by: kyle7 ]
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nobody
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posted 16. February 2003 13:10
quote:
When we attain this level of technology, I think the notion of ID will gain momentum as we begin to discover the complexity of life.
Two quick points:
1. I don't know if humans will ever reach the level of technology you describe. I would like to think we are smart enough to eventually get there, but the future is not easily predictable.
2. Getting back to Shapiro, he seems to say that we are discovering the "complexity of life" right now. I agree. Except I call it the programming of life.
Sixty years ago humans would have had no idea what our discussion in this thread even meant. Now we (many of us) have programming all around us so we tend to take it for granted. Behind each and every programmed system in your life is intelligence. In other words, they are the result of an intelligent programmer. So, in 2003, we can at least recognize the programming of life for what it is, although it is still beyond our capability to fully understand how it functions.
It's kind of like when the Rosetta Stone was found. The people who looked at it recognized it for what it was, but they were not immediately able to translate it. Fully understanding the programming of life, if it's even possible, will require years from our best companies, our best computers and our best programmers.
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Mike Gene
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posted 16. February 2003 21:35
Nobody: It's kind of like when the Rosetta Stone was found. The people who looked at it recognized it for what it was, but they were not immediately able to translate it. Fully understanding the programming of life, if it's even possible, will require years from our best companies, our best computers and our best programmers.
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. As Shapiro notes,
quote:
The best current metaphor for how the genome operates is to compare it to the hard drive in an electronic information system and think of DNA as a data storage medium. The metaphor is not exact, in part because genomes replicate and are transmitted to progeny cells in ways that have no precise electronic parallel. Nonetheless, the information-processing metaphor allows us to view the role of the genome in a realistic context. DNA by itself is inert. Information stored in genomic sequences can only achieve functional expression through interaction of DNA with other cellular information systems (Table 3).
Here is another site that might interest some:
quote:
Viewed as information processing systems, biological organisms possess amazing capabilities to perform information-handling tasks such as: control, pattern recognition, adaptability, information-storage, etc. Thus, the functioning of biological organisms as information-processing systems is of great interest to computer scientists, and we are witnessing now a fast growing research in this field. This research is genuinely interdisciplinary in nature, involving both computer scientists and molecular scientists (biologists, biochemists, biophysicists, crystallographers, …). One of the leading paradigms of this research is “cell as a computer”. A beautiful example of this paradigm is a single cell organism called ciliate – the gene assembly process in ciliates has turned out to be a very elegant computational process which even uses one of the basic data structures of computer science: the linked lists! This process of gene assembly (assembling genes of macronucleus from their micronuclear form) is the most involved DNA processing known in living organisms.
What ID needs today is more extensive cross-talk between biologists, computer programmers, and engineers. Computer programmers and engineers explain their craft, and biologists look for the familiar. Biologists explain their craft, and programmers/engineers look for the familiar. No conclusions of "design," just looking, probing, feeling....
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Mike Gene
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posted 16. February 2003 23:06
Hi Gedanken,
You write: 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.
Yes, this is always a possibility and there will always be plenty of people to flesh it out. The alternate possibility that I am trying to explore is that the reason communication theory (and engineering concepts, BTW) seem to apply especially to biology is because they all stem from a common cause. While an asteroid hitting the moon can be viewed as imparting "information" from the standpoint of communication theory, those who study asteroids are not dependent on this approach. Biologists, in contrast, seem to be drawing deeper and deeper from this approach, with greater and greater payoffs.
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Mike Gene
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posted 17. February 2003 21:58
I searched two databases full of scientific articles, Biological Abstracts and GeoRef:
quote:
Biological Abstracts, a leading source of life science information, collects abstracts and bibliographic references to worldwide biological and medical literature. Biological Abstracts contains references to journal items focusing on vital biological and medical research findings, pharmacological studies, and discoveries of new organisms. Approximately 5,500 international journals are reviewed for inclusion, representing virtually every life science discipline.
and
quote:
The GeoRef database, established by the American Geological Institute in 1966, provides access to the geoscience literature of the world. The database contains references to geoscience journal articles, books, maps, conference papers, reports and theses. The GeoRef database covers the geology of North America published from 1785 to the present, and the geology of the rest of the world published from 1933 to the present. The database includes references to all publications of the U.S. Geological Survey. Masters' theses and doctoral dissertations from U.S. and Canadian universities are also covered. To maintain the database, GeoRef editor/indexers regularly scan more than 3,500 journals in 40 languages as well as new books, maps, and reports. They record the bibliographic data for each document and assign index terms to describe it. Each month between 4,000 and 7,000 new references are added to the database.
I first searched both databases with the term 'energy,' since this is a concept we might expect to be equally important in both biology and geology. Biological Abstracts returned 230280 hits, while GeoRef returned 199059. I then searched both databases with terms (and exact phrases) we might expect to find in a field of technology. Listed below are the search terms followed by the number of hits from Biological Abstracts and GeoRef, respectively.
AMPLIFY 6494 74
ADJUST 4768 193
CIRCUIT 11821 268
CIRCUITRY 3505 24
CHECKPOINT 2665 0
COMMUNICATE 1799 123
COMPENSATE 8281 243
CORRECT 35567 1823
DAMPEN 301 16
EDITING 1978 263
ENCODE 17855 4
ERROR 35317 3996
EXPRESS 53368 516
FIDELITY 4219 156
MESSAGE 6897 137
NODE 43096 271
PROOFREADING 589 0
QUALITY CONTROL 8405 1615
REGULATE 44413 127
SHORT CIRCUIT 2863 15
SUPPRESS 23160 160
TRANSLATE 1971 101
TRANSMIT 3655 145
[ 17. February 2003, 22:00: Message edited by: Mike Gene ]
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gedanken
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posted 18. February 2003 00:31
Mike Gene said:
quote:
Yes, this is always a possibility and there will always be plenty of people to flesh it out. The alternate possibility that I am trying to explore is that the reason communication theory (and engineering concepts, BTW) seem to apply especially to biology is because they all stem from a common cause. While an asteroid hitting the moon can be viewed as imparting "information" from the standpoint of communication theory, those who study asteroids are not dependent on this approach. Biologists, in contrast, seem to be drawing deeper and deeper from this approach, with greater and greater payoffs.
Mike, you may be surprised to know that I agree with every word you wrote in that paragraph. By that, I mean that I agree with the meaning as I read it, and I am choosing to read it in a way that may be taken as a bit more broad than you may have meant when writing the paragraph.
For example let me present a more or less philosophical viewpoint on the creation and nature of the universe -- one possible philosophical stand: This is a somewhat Eastern position. The position is that the universe is a manifestation of God trying to find himself. In this view, the universe is not “designed” by an external god, rather the universe itself is a manifestation of God and physical reality designing itself. I present this as an alternate to various views of ultimate causation, to demonstrate that forms of “common cause” can vary from a “design” by intelligence to universe becoming intelligence.
The reason I bring this up is the question of whether noting a common cause has anything to do with distinguishing by observation whether that common cause has anything to do with external design beyond or outside the properties of those systems themselves.
In 1945 the French mathematician Hadamard said:
quote:
We shall see a little later that the possibility of imputing discovery to pure chance is already excluded. . . . Indeed, it is obvious that the invention or discovery, be it in mathematics or anywhere else, takes place by combining ideas.
-- J. Hadamard
(This is a quote I found referenced in a “Genetic Programming” book.)
If one presupposes evolution processes as working alone in the physical world and physical dimension of reality being studied, then one has a consistent view based on observation, and the notions of engineering terms being usefully applied to biological organisms. I recommend again reading from 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.
Now consider a different presupposition -- that there is an ultimate design inherent in the universe. From this precept, we don’t have a contradiction in the physical dimension of reality, as we still have consistency with observation if we examine design as a natural phenomenon of evolution, and a natural capacity of physical human beings and other organisms.
In other words there is no distinction between saying that engineering terms like “information” are useful in describing biological systems, and saying that biological systems have complex interoperating parts. All possible systems that have complex interoperating parts will have useful applications of engineering terms like “information” in their description -- and the more complex, the more useful. So in that respect there is no new observation in the applicability of engineering terms beyond the observation of complexity of varied interoperating parts. Noting their common origin is to note their commonality in the evolutionary process.
Now going back to the philosophical considerations of design or non-design of the universe (from varying perspectives), we see that this level of question is not distinguished by the noting of the complexity of interoperating parts in the systems found within the universe. There are very deep questions of why the universe would tend to produce beings that can understand the universe itself. And based on starting philosophical assumptions, I think that observation combined with the starting philosophical assumption can be illuminating.
But speaking in terms of what can be distinguished by observation of the physical world alone, and based broadly and independently of philosophical assumptions, I think we find a couple of things: That the commonality of the origin of engineering concepts and of descriptions of biological assumptions is extremely reasonable and in fact expected. However that there is commonality does not lead to distinguishing the nature of that commonality as design by an external agent, as all human engineering design is done by human beings operating within physical reality and subject to observation as such.
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nobody
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posted 18. February 2003 12:27
Mike Gene makes a suggestion:
quote:
What ID needs today is more extensive cross-talk between biologists, computer programmers, and engineers.
I agree. But then I'm curious about almost everything. It seems to me, as an outsider looking in, that many specialties have now grown so complex that almost all of a person's time is spent within their own sometimes narrow specialty just to keep up with the massive flow of information.
How do we encourage this cross-talk? Is this a possible function of ISCID?
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Janitor@MIT
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posted 18. February 2003 13:01
“Communication theory has very little to with semantic meaning (in the sense that no considerations of semantic meaning is made in communication theory… Therefore you need to elaborate how thinking in terms of communication theory amounts to a strongly teleological viewpoint.”—Erik
This would seem to be supported by Shannon’s own prefatory disclaimer (“These semantic aspects of communication are irrelevant to the engineering problem…”), but in fact he can’t escape the problems semantics poses for any theory of communications. Semantics are written all over this theory. E.g., why, in your own post are there stipulations to efficiency and fidelity, which also would seem to be the central problems addressed by Shannon? Clue: “Frequently the messages have meaning; that is they refer to or are correlated according to some system with certain physical or conceptual entities (Claude Shannon, “A Mathematical Theory of Communication,” 1948, p. 1. Emphasis in original.).” The stipulations are given and central to communications theory purely because messages have meanings. The principle problem of communications engineering is not the transmission of information. It is the transmission of meaningful information. The transmission of meaningless information is purely unproblematic and requires no theory.
What makes a message meaningful, obviously, is not merely a question of how faithfully and efficiently it is reproduced, but exactly how faithfully and efficiently it is “correlated according to some system with certain physical or conceptual entities.”
Shapiro’s articles cited by Mike Gene begins to address the existence of that “semantical system.” Basically the problem for communications engineering is identical to the problem of living: how to encode, transmit, decode, and further process for re-transmission a message that must be correlated faithfully and efficiently to the physical entities that the information represents. This is meaningful because it is exactly the problem of survival, reproduction, adaptation, and evolution.
(Its ironic to consider that science must in some way be about the meaningful statements we can make about our world, and ourselves but science is possessed of no generally recognized, coherent, and comprehensive theory of meanings. It is interesting to compare the use of “semantics” in design theory, where it is the central problem of analysis and design, as indicative of sets of characteristic equations. The “semantics” of a system are its solutions.)
“I recommend again reading from 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.”—Gedanken
I believe you’ve got this backward. Wiener’s original research conducted under the auspices of the War Department was on weapons control systems, which inspired his investigations into biological (specifically neurological) control. Its been many, many years since I’ve read Cybernetics, but hazarding error upon error, I recall that almost all the book treated in time series analysis the control of target acquisition and tracking, and comments about biology were largely confined to the afterwords (?). The concepts of control entered molecular biology in the early 1950’s, although its formal roots in engineering go back to the early-mid 19th century. Of course controls are fundamental to designing and conducting experiments, but even so natural scientists made no connection.
Its difficult to imagine why the use of “teleology” is so objectionable for biologists, as control is now a central principle there, and a control would seem to be definitively “teleological.”
See Jacques Monod’s Chance and Necessity (1971) and especially the first chapter “Of Strange Objects,” for an intriguing discussion, “Every artifact is a product of a living being which through it expresses, in a particularly conspicuous manner, one of the fundamental characteristics common to all living beings without exception: that of being objects endowed with a purpose or project, which at the same time they exhibit in their structure and carry out through their performances (such as, for instance, the making of artifacts). Rather than reject this idea (as certain biologists have tried to do) it is indispensable to recognize that it is essential to the very definition of living beings. We shall maintain that the latter are distinct from all other structures or systems present in the universe through this characteristic property, which we shall call teleonomy. But it must be borne in mind that, while necessary to the definition of living beings, this condition is not sufficient, since it does not propose any objective criteria for distinguishing between living beings themselves and the artifacts issuing from their activity (Emphasis in original.).”
“In other words there is no distinction between saying that engineering terms like “information” are useful in describing biological systems, and saying that biological systems have complex interoperating parts. All possible systems that have complex interoperating parts will have useful applications of engineering terms like “information” in their description -- and the more complex, the more useful. So in that respect there is no new observation in the applicability of engineering terms beyond the observation of complexity of varied interoperating parts.”—Gedanken
Gedanken, it sounds as if you think this is a simple problem?! This is also incorrect. The application of information theory generally to engineering design (which is the problem of defining the reciprocating functions/operators, the interconnections, interoperability, of combinatorial objects—i.e. the very problem of control) has not been made until recently: “In view of this compelling information-based description of control units [sensors and actuators], it is perhaps surprising to note that few efforts have been made to go beyond the intuitive and qualitative aspects of it to develop a quantitative theory of controllers focused explicitly on information… there exists at present no general information-theoretic formalism characterizing the exchange of information between a controlled system and a controller, and more importantly, which allows for the assignation of a definite value of information in control processes. To address this deficiency, we proceed in this paper with a detailed study of an attempt for such a formalism (Touchette, H. & S. Lloyd, “Information-Theoretic Approach to the Study of Control Systems,” Submitted to IEEE non Information Theory, Vers. of 12/12/01. Emphasis in original.)…” See the citations for previous work along these lines.
(See also Jan Willems landmark, “Paradigms and puzzles in the theory of dynamical systems,” IEEE Transactions on Automatic Control, Vol. 36,pp. 259-294, 1991 and “On interconnections, control, and feedback,” IEEE Transactions on Automatic Control, Vol. 42, pp. 326-339, 1997.)
I don’t suppose that it can be emphasized enough just how far Shapiro is departing from traditional theory here. (Although he may be hesitant to admit it.) But received theory has always been rather vague and self-contradictory wrt to the real possibility that life forms are possessed of systems that exercise some effective control over their own adaptation and evolution. How it could be otherwise is difficult for me to even imagine.
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Mike Gene
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posted 18. February 2003 13:32
Gedanken: In other words there is no distinction between saying that engineering terms like “information” are useful in describing biological systems, and saying that biological systems have complex interoperating parts. All possible systems that have complex interoperating parts will have useful applications of engineering terms like “information” in their description -- and the more complex, the more useful. So in that respect there is no new observation in the applicability of engineering terms beyond the observation of complexity of varied interoperating parts. Noting their common origin is to note their commonality in the evolutionary process.
But speaking in terms of what can be distinguished by observation of the physical world alone, and based broadly and independently of philosophical assumptions, I think we find a couple of things: That the commonality of the origin of engineering concepts and of descriptions of biological assumptions is extremely reasonable and in fact expected. However that there is commonality does not lead to distinguishing the nature of that commonality as design by an external agent, as all human engineering design is done by human beings operating within physical reality and subject to observation as such.
Like I mentioned above, this is one way to look at it. The commonality may also be traced to the fact that life is technology. And the fact that concepts derived from enhancements in our own technology allow us to unlock the workings of cell supports this view.
The standard view of the cell is that it is the product of geochemistry. This is also why it is interesting to note that the technological terms/concepts that unlock the working of the cell do have the same level of utility in geoscience, as shown by the Biological Abstracts/Geo Ref survey above.
Things get even more interesting if we search the database, INSPEC, which "provides access to the world's scientific and technical literature in physics, electrical engineering, electronics, communications, control engineering, computers and computing, and information technology." Here's a couple of examples.
Take the term checkpoint. While it is not found in GeoRef, and used 2665 times in Biological Abstracts, it is also found 728 times with INSPEC. Janitor says:
quote:
Basically the problem for communications engineering is identical to the problem of living: how to encode, transmit, decode, and further process for re-transmission a message that must be correlated faithfully and efficiently to the physical entities that the information represents.
Let's take the terms 'encode,' 'transmit,' and 'decode' and consider the number of times each is cited in these three databases.
ENCODE
Bio Ab - 17855
INSPEC - 3859
GeoRef - 4
TRANSMIT
Bio Ab - 3655
INSPEC - 14785
GeoRef - 145
DECODE
Bio Ab - 196
INSPEC - 1738
GeoRef - 6
Clearly, a pattern begins to appear where biology and technology converge to the exclusion of geology. In fact, my thesis makes a distinct prediction here - the pattern of convergence between biology and technology, to the exclusion of the other physical sciences, will expand and intensify. If you think about it, the approach to biology that is advocated by Shapiro will turn biology into a field of inquiry that cannot be distinguished from human technology, but is different from the study/understanding of volcanoes, crater impacts on the moon, and tornadoes, even though the latter are quite complex. And this takes us back to the observations from Davies (which are from the Fifth Miracle ).
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Mike Gene
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posted 18. February 2003 13:52
Nobody: How do we encourage this cross-talk? Is this a possible function of ISCID?
It would seem to be something worth considering. Imagine a conference where biologists simply describe the workings of the cell. Computer scientists and engineers soak it in to determine if this talk is alien or familiar. Repeat with a day of seminars where computer scientists talk about programming. Biologists soak it in to determine if this talk is alien or familiar. Repeat with the engineers. The ID community should begin to establish cross-talk between its members from these three fields, and from here, expand outward. For example, I have come across several ID proponents on the web who, while lacking in biological knowledge, are computer programmers. These people have an important and active role to play in ID which isn't being tapped (IMO), where they can draw from their own fields of expertise to inform the biologists. Consider the statement from the above link:
quote:
A beautiful example of this paradigm is a single cell organism called ciliate – the gene assembly process in ciliates has turned out to be a very elegant computational process which even uses one of the basic data structures of computer science: the linked lists!
A conference where a biologist is speaking, only to have a computer scientist/engineer arrive at such a "eureka" moment, would be quite helpful for all.
Keep in mind that ID predicts there is special common ground between the biologists, engineers, and computer programmers. Thus, we can further predict that more intense cross-talk between the groups would not only produce fruit, but a track record of fruit.
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nobody
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posted 19. February 2003 00:23
Mike Gene says:
quote:
1. A conference where a biologist is speaking, only to have a computer scientist/engineer arrive at such a "eureka" moment, would be quite helpful for all.
2. Keep in mind that ID predicts there is special common ground between the biologists, engineers, and computer programmers. Thus, we can further predict that more intense cross-talk between the groups would not only produce fruit, but a track record of fruit.
Hi Mike,
1. I'm a little surprised this hasn't been done yet. What can be done to encourage a conference of this type? This seems like an excellent way for making significant progress.
2. Thanks. I like predictions. I think you've just made a very compelling argument for anyone who is currently undecided about the highly intelligent design of life.
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gedanken
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posted 19. February 2003 01:06
Janitor@MIT said:
quote:
I believe you’ve got this backward. Wiener’s original research conducted under the auspices of the War Department was on weapons control systems, which inspired his investigations into biological (specifically neurological) control.
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. Second that early in development of control systems (e.g. Wiener’s work) that commonality that Mike is talking about was recognized. (I am in fact agreeing with Mike in a sense about the common roots of both.) I am completely in agreement that the reasons for the work on control theory are motivated by need for construction of devices (e.g. military). This in no way contradicts my thesis. That the commonality was recognized so early and naturally in development of advanced control and information theory is the basis of my agreeing with Mike on this point, and of my claim of the relevance of reading Wiener. In no sense am I claiming that the first application of such theory was in understanding of the biological system -- rather that the primitive notions of control themselves, needing theoretical analysis, are based on the observation of biological systems in their root, and that the primitive (unrefined) versions of these control systems had this genesis. Though not stated, one can get a sense of this by reading Weiner. Then of course the first application of the more advanced theory was in the type of construct that offered both simplified relationships and motivation.
quote:
Gedanken, it sounds as if you think this is a simple problem?! This is also incorrect. The application of information theory generally to engineering design (which is the problem of defining the reciprocating functions/operators, the interconnections, interoperability, of combinatorial objects—i.e. the very problem of control) has not been made until recently: …
But this gets back to that same issue of whether application and origin are congruous. Clearly Shannon (whom you mention first) was developing communication and information theory because of suspected technological applications -- from his very first inception of those notions.
If you think that the writer quoted would be correct in general terms about control theory being recognized as applicable to understanding of biological system (such as near the year 2001), then I highly recommend reading Weiner (who’s book was initially copyrighted more than half a century before). That writer may have been commenting about an aspect, but to claim that such a detail implies the general would be misleading.
Mike Gene said:
quote:
Like I mentioned above, this is one way to look at it. The commonality may also be traced to the fact that life is technology. And the fact that concepts derived from enhancements in our own technology allow us to unlock the workings of cell supports this view.
The standard view of the cell is that it is the product of geochemistry. This is also why it is interesting to note that the technological terms/concepts that unlock the working of the cell do have the same level of utility in geoscience, as shown by the Biological Abstracts/Geo Ref survey above.
I completely agree that life is technology, because I identify the processes of evolution as producing design.
A useful concept: “Data” becomes “information” when it is interpreted. A command cannot be acted upon until it is “understood”. But what is “understanding”? This differs with the level of complexity of a system. A primitive electronics control system “interprets” a command “GO”, given by a contact closure, in an extremely simple manner. Yet the “data” of the contact closure bit becomes “information” when it is interpreted by the simplistic control system. We can go both ways (in degrees of complexity) from this analogy. To go up, we have the interpretation of complex language (either by machine or even and much more subtly by a human). A little bit up the scale we have compilers and such instruments that translate reasonably complex (though highly structured) language and “interpret” them according to their nature. Further up the scale are complex animals that interpret visual cues as useful in hunting for food and avoiding danger. And of course at the top of our experience is ourselves, the human, with obvious degrees of complexity in data and its interpretation.
Now go the other direction. A rock delivers an impact -- a “transmission” of momentum and energy. Little need is found for information theory as the situation is in relative terms so simple. It is the complexity of the processes of interpretation that give rise to the requirements of information theory. This goes along with the complexity of the system itself (with a certain view of complexity). The “complexity of varied interoperating parts” in a system is directly related to the complexity of that system’s processes of interpretation of stimuli, whether viewed as simply energy considerations or as causes based on intention as a measured by some completely separate association with an external intelligent agent.
My principle point was that having agreed that life is technology, what are you trying to imply beyond that point? And if you have implications beyond that, how are dimensions of that further implication teased out by observation of the physical world?
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