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Author
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Topic: Shapiro on the Genome
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nobody
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Member # 145
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posted 19. February 2003 11:58
quote:
1. I completely agree that life is technology,
2. because I identify the processes of evolution as producing design.
1. Very good to have you on "our" side. ![[Wink]](wink.gif) It seems completely obvious, yet I have seen some disagree in the past. Do you also agree that the technology of life is more advanced than the current technological capability of human scientists?
2. I see. Then I have a question: What specific design can you scientifically prove was ever produced by the "processes of evolution"?
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Moderator
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posted 19. February 2003 12:16
Nobody,
You were provided with a warning. You are now being banned for one day. You need to stop playing the "advocate."
Contact me at moderator@iscid.org
[ 20. February 2003, 11:14: Message edited by: Moderator ]
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nobody
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posted 21. February 2003 15:14
Mike Gene said:
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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.
That's a very important, and often overlooked, point about the software, imo. Great hardware without any software is useless.
Below is another instance of attempting to reverse engineer a part of life. In this case it's the human brain, the most powerful computer known to science. Some people believe this reverse engineering goal can be reached within 30 years....
http://www.discover.com/dec_02/feattech.html
Reverse-engineering the brain might finally lead to smarter computers
By Chip Walter
Kwabena Boahen, a lead researcher at the University of Pennsylvania's Neuroengineering Research Laboratory, has a love-hate relationship with the gray matter between his ears. He ardently admires the subtlety of the brain's design: "Very elegant and much more efficient than anything I could come up with," he says. But for an engineer, admiration is not enough; he and his colleagues want to understand the brain's mechanisms and re-create its functions in a lab. In this effort, the elaborate nature of the neuronal programming that transforms electrical currents into thought and perception is a source of endless frustration. "Everyone is banging their heads up against this complexity issue," Boahen says.
* * * * *
It will be fascinating to watch the progress of some of these attempts, but I believe they will be unable to fully reverse engineer the human brain. They might be able to map out all the hardware eventually and create a copy, but they won't have any software capable of running on the artificial brain. Of course, I could be proven wrong some day in the future.
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gedanken
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posted 22. February 2003 00:04
On page 1 of this discussion, I make the point that there is no “software” independent of a representation in hardware. In fact this distinction is artificial. No discussion of this point has happened as far as I can tell.
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nobody
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posted 22. February 2003 13:19
Well....
On page 1 you claim:
quote:
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.
You argue that there is information being imparted by an asteroid hit. This view appears to be nearly identical to the thread at ARN claiming there is information in a snowflake. Actually there is no information you can retrieve from a snowflake, or in an asteroid impact. You can write up a very complex description ABOUT a snowflake, but there is no information contained IN a snowflake.
In contrast to your position about information is the position of most scientists I have seen comment on the subject. Here's just one from a quick google search:
The Human Genome: Information Content and Structure
DENNIS W. ROSS
University of North Carolina
At a length of two meters and a width of two billionths of a meter, the genome amounts to a library whose code letters carry complete instructions for building and maintaining a human. Until recently, the code was modified only by mutation and natural selection. Today, however, we possess the technology to read and write DNA. The consequent knowledge is already changing medical practice.
--------------------------------------------------------------------------------
Dr. Ross is Clinical Professor, Department of Pathology, University of North Carolina at Chapel Hill School of Medicine and Wake Forest University School of Medicine, Winston-Salem.
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Within every cell in the human body is the information required to make an entire human being. The information is the human genome, written in DNA as a string of three billion code letters--or rather, six billion, considering that each cell has two versions. Determining a complete representative sequence constitutes the greatest scientific enterprise of our time, a task expected to be completed early in the new millennium. We must then expand our efforts to understand and utilize the information, which (to use a familiar measurement of data storage) would fill 10,000 floppy disks.
* * * * *
The Dr. is not talking about a description of the physical structure of DNA. He is talking about the information contained within the DNA code. We can't fully understand this software yet, but we're working on it.
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RBH
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posted 22. February 2003 13:42
I think nobody missed the main point of gedanken's earlier posting in this thread. gedanken wrote that quote:
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.
As I read it, that means that the notion of abstract "information" existing independently of a physical instantiation or manifestation is a description of (i.e., is about) physical systems but is not in itself some sort of entity or causal force. This line of argument is parallel to that of the late Rolf Landauer, who argued that information could not be understood independent of (in isolation from) its physical embodiment.
nobody's quotation from Ross is doubtless interesting, if not novel, but doesn't contradict gedanken's point as far as I can tell. Ross is specifically writing about information embodied in the DNA, not about some abstract notion. And that was gedanken's point, or at least a major part of it.
RBH
[ 22. February 2003, 13:44: Message edited by: RBH ]
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gedanken
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posted 22. February 2003 16:49
With regard to my point, but changing the subject slightly:
What is information? I think that the term needs to be defined somewhat (and I’ll wait for others, as I think I have given a partial definition in terms of something that is interpreted by another process, without at this point further defining “interpret”.)
For example, does “information” have to originate with an intelligent agent a priori in order to be defined as “information”? In that case then we have no knowledge of any information in a “snow flake” as ‘nobody’ said. But if, as Shapiro’s paper seems to allude, there is communication of information from one point to another in the biological organism as feedback and control systems operate, then we have a definition that is in terms of mechanistic function and having nothing to do with an intelligent agent as source or as destination of the message. This would be compatible with my thought, saying that something can be considered information when it is interpreted by another system. (And in this case in the biological organism, “interpret” is taken very liberally as a process acting on the “message” -- and the presence of “acting upon” make the message “information”, and “acting upon” is what I mean by “interpret”.)
What other meanings are there for “information” that are compatible with the notion of communication within an organism?
[ To RBH, actually I may have mixed aspects together, I’ll go back and look. The notion of the abstraction as distinct from the concrete is extremely important. In fact in my concept, “interpret” is a concept of our description or mental model of how the system operates, but the physical system just operates according to the relations of physics whether or not our mental model is accurate. So at one level I mean to separate the concept of information from the physical system. But at another level I want to do the opposite -- define “information” as a physical process rather than a description of an abstraction of that physical process. (All communication in the real world uses energy, I think we would all agree.) The element of abstraction is still necessary and important, but in this case I am trying to identify “information” as physical energy that has that property of the abstract classification according to the mental model of being interpreted by another system. I guess my point will be that one has to choose -- is “information” the mental abstraction itself, or is “information” a form or description of energy? ]
[ 22. February 2003, 17:01: Message edited by: gedanken ]
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Mike Gene
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posted 22. February 2003 18:16
Gedanken: I completely agree that life is technology, because I identify the processes of evolution as producing design.
That's fine. My hunch is that evolution is the product/output of design. Or better yet, an intelligence has designed life to exploit and channel evolutionary processes. Like I said above, this all boils down to perspective.
A useful concept: “Data” becomes “information” when it is interpreted.
Which is why all "evidence" has a subjective component (something to keep in mind when requests for "evidence" are made).
A command cannot be acted upon until it is “understood”.
Yes. Which is why I often ask what type of data people would consider "evidence" of design. ![[Smile]](smile.gif)
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.
Which brings us to an interesting point. The concept of proofreading, for example, applies at all levels of life. For example, we'd probably say that a mammal is relatively more complex than a bacterium, but this information concept applies to both. In contrast, I'm not sure there are any information theory concepts that a mammalian-specific. In other words, the technological concepts mentioned above not only appear to be relatively unnecessary in geoscience, but describe universal features of life, applicable from bacteria to humans.
My principle point was that having agreed that life is technology, what are you trying to imply beyond that point?
Two things. First, the concept that life is designed passes an important falsification test. If life was designed by a human-like intelligence, we would expect it to cluster with things known to be designed. For example, it was originally thought that we could understand the workings of the cell without appealing to its machines. But we can't.
Secondly, the view that life is technology, or the expression of bioengineering, provides a rich template for experimental exploration. For example....
And if you have implications beyond that, how are dimensions of that further implication teased out by observation of the physical world?
I already mentioned one thing above - 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. This prediction follows from the hypothesis that life is advanced technology. Thus, as our own technology advances, we will better appreciate what is going on inside life.
Furthermore, I would suggest that my explorations of cytosine deamination and its effects mediated by the genetic code come into play here (as a nice illustration). The interpretative perspective that you advocate appears to lack the "probing power" that mine has.
PS: BTW, there's more to add with the cytosine deamination story. Look for it next month.
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RBH
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posted 22. February 2003 20:34
The first question and answer in the ISCID chat with Shapiro the other day struck me as interesting. They were: quote:
Bill Dembski
James, we met the first time at Wheaton College at a symposium in the spring of 1997 featuring principally you and Michael Behe along with Paul Nelson and David Hull. At the time I asked you about the origin of such "natural genetic engineering" systems. As I recall, you indicated that this was not really the problem you were addressing. Have you thought any more about this problem? Specifically, how do such systems arise that can take over their evolution? And how much complexity do they require? Are you confident that non-teleological mechanisms can account for the rise of natural genetic engineering systems, and if so why?
James Shapiro
I am not sure how to answer your question. All existing living organisms possess natural genetic engineering capabilities. So they must be pretty fundamental. Any self-organizing evolving system has to have the capacity to alter its information store. That's what they do. Where they come from in the first place is not a question we can realistically answer now, any more than we can explain the origin of the first cells.
I got curious about what the "natural genetic engineering capabilities" are and whether they themselves might be evolvable. One hears about the "evolution of evolvability," and natural genetic engineering tools seem to me to be that sort of thing. While molecular biology is outside my competences, nevertheless the question is accessible given some reading and thought. Reading Shapiro, particularly the chat, I thought about stress-induced hypermutational activity, too, but decided to stick to the evolvability of tools for this posting.
In A 21st Century View of evolution on his web page Shapiro identifies his approach as non-Darwinian. (Parenthetically, it's not altogether clear what Shapiro means by "Darwinian" but the implicit meaning, given his off-hand remarks in several papers, seems to be gradualist-one-mutation-at-a-time-little-bitty-steps-incrementalism, sort of like the caricature of Dawkins' position one often sees.) Whatever his conception of "Darwinian," it is clear that he believes that the natural genetic engineering toolbox he writes of is non-Darwinian. The question that interests me, though, is whether the tools themselves could have arisen in Darwinian fashion.
In "A Third Way (Alternatives to Creationism and Darwinism)," Shapiro identifies four major categories of advances in molecular biology that open the way to his 21st Century approach. Very briefly, they are: quote:
(These are not quotations; I use the quoting facility to set them off for ease of reading)
1. The finding that genomes are organized above the individual gene level. Chromosomes are not merely strings of genes organized as 'beads on a string.' Several organizational principles seem to govern the arrangements of genes.
2. The discovery of cellular repair systems that act to correct errors of various sorts in genes, including many due to mutations of various kinds. Shapiro writes "It has been a surprise to learn how thoroughly cells protect themselves against precisely the kinds of accidental genetic change that, according to conventional theory, are the sources of evolutionary variability."
3. The discovery of "mobile genetic elements," DNA structures that move from one location to another in genomes. Among these are retrotransposons, gene fragments assembled by lymphocytes, nucleases, ligases, reverse transcriptases, and polymerases, a veritable potpourri of mobile elements.
4. The reconceptualization from genes-as-coding-for-traits to gene complexes as encoding information. Shapiro writes of "the growing realization that cells have molecular computing networks which process information about internal operations and about the external environment to make decisions controlling growth, movement, and differentiation." The anthropomorphism of "make decisions" aside, Shapiro's point seems to be consistent with the notion of molecular systems that process (biochemical) inputs in non-trivial ways to produce an output 'selected' from an array of possible outputs. Information processing here seems to mean transforming inputs according to the interactions of a (large) number of biomolecules.
A relevant question is whether the various advances Shapiro identifies as underpinning a new theory of evolution and change in cellular functioing are themselves the products of regular old Darwinian processes. That question seems to fall under the 'evolution of evolvability' rubric, so it was under that heading I first searched. And sure enough, there are indications that at least one of the advances Shapiro writes of, the organization of the genome, is itself evolvable.
For example, John W. Pepper's The Evolution of Evolvability in Genetic Linkage Patterns suggests that "clustering of epistatically interacting genes increases the rate of adaptation." Pepper writes quote:
Abstract:
A number of factors have been proposed that may affect the capacity for an evolutionary system to generate adaptation. One that has received little recent attention among biologists is linkage patterns, or the ordering of genes on chromosomes. In this study, a simple model of genetic interactions, implemented in an evolutionary simulation, demonstrates that clustering of epistatically interacting genes increases the rate of adaptation. Moreover, long-term evolution with inversion can reorganize linkage patterns from random gene ordering into this more modular organization, thereby facilitating adaptation. These results are consistent with a large body of biological observations and some mathematical theory. Although linkage patterns are neutral with respect to individual fitness in this model, they are subject to lineage-level selection for evolvability. At least two candidate mechanisms may contribute to improved evolvability under epistatic clustering: clustering may reduce interference between selection on different traits, and it may allow the simultaneous optimization of different recombination rates for gene pairs with additive and epistatic fitness effects.
It may not be necessary to argue for selection at the lineage level as Pepper does. In a study of the possibility of the genetic code itself evolving (On the Evolution of Primitive Genetic Codes ), Weberndorfer, Hofacker, and Stadler write quote:
In this contribution we describe detailed mechanistic simulations of a simplified (proto)organism that show that the genetic code can indeed evolve in the presence of strong selection on the encoded polypeptides. This approach differs from previous arguments for the adaptive nature of the code [e.g., Pepper's] in that we need not assume a direct selection pressure on higher order properties such as evolvability. Indeed, our model is based on the reproductive success of individuals which depends only on the quality of the encoded proteins, not on the code that they use. The evolution of the encoding is therefore an emergent property in our model. (p. 4)
Finally, there is a body of work suggesting that the mapping of genes to phenotypes, and the associated developmental processes, are under evolutionary control. Toussaint writes quote:
In nature, phenotypic variability is highly structured with respect to correlations between different phenotypic traits. In this paper we argue that this structuredness can be understood as the outcome of an adaptive process of phenotypic exploration distributions, similar to the adaptation of the search distribution in heuristic search schemes or Estimation-of-Distribution Algorithms. The key ingredient of this process is a non-trivial genotype-phenotype mapping: We rigorously define non-triviality, in which case neutral traits (as a generalization of strategy parameters) influence phenotype evolution by determining exploration distributions. Our main result is the description of the evolution of exploration distributions themselves in terms of an ordinary evolution equation. Accordingly, the "fitness" of an exploration distribution is proportional to its similarity (in the sense of the Kullback-Leibler divergence) to the fitness distribution over phenotype space. Hence, exploration distributions evolve such that dependencies and correlations between phenotypic variables in selection are naturally adopted by the way evolution explores phenotype space. (emphasis added)
And in the context of evolving autonomous agents, Dellaert and Beer write quote:
Abstract
We are interested in the synthesis of autonomous agents using evolutionary techniques. Most work in this area utilizes a direct mapping from genotypic space to phenotypic space. In order to address some of the limitations of this approach, we present a simplified yet biologically defensible model of the developmental process. The design issues that arise when formulating this model at the molecular, cellular and organismal level are discussed, and for each of these issues we describe how they were resolved in our implementation. We present and analyze some of the morphologies that can be explored using this model, specifically one that has agent-like properties. In addition, we demonstrate that this developmental model can be evolved.
There are other papers relevant to the general question, but these are sufficient to illustrate the point: Darwinian evolution is not limited to the replacement of one base at a time in hopes of finding something selectively advantageous. Higher-level properties of genetic encoding themselves appear to be evolvable by neoDarwinian means. Thus the "non-Darwinian" processes Shapiro invokes may be themselves the product of Darwinian processes.
The papers cited are not dispositive, of course; at best they are suggestive. At the least, though, the conclusion that the kinds of processes Shapiro identifies require a non-Darwinian evolutionary theory is premature. However, as long as he hangs onto the "natural" in "natural genetic engineering," I'm not uncomfortable. There's interesting stuff there, and it will be fun to see how it plays out over the next decade or so.
RBH
[ 22. February 2003, 20:41: Message edited by: RBH ]
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gedanken
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posted 22. February 2003 21:00
MikeGene said:
quote:
The interpretative perspective that you advocate appears to lack the "probing power" that mine has.
First let me address “proofreading”. That is not so much a feature of “information theory” as it is a method of correcting errors. As such it can be classified amongst a large class of methods in information processing, and as such I suppose part of “information theory”. But this gets back to my point that such concepts are abstractions of what the biological system really does. I suggest that it does something approximately like what might be viewed as “proofreading”, by some rather mechanistic means. This is what I mean that the system is processing physical matter and energy, not abstract “information”. The kind of “information” that is being dealt with is one that must be considered in the physical realm of physical action -- and only exists in the form of an abstraction like “proofreading” when viewed as an abstract model. Abstract models are creations of human intelligence, and are not the actual workings of the biological organism. So my suggestion is that “proofreading” is actually a physical process that reminds the human in abstraction of proofreading a text.
Now the “interpretive” perspective is meant to show that we have notions that are near to each other in meaning. I don’t think that there is any absolute meaning in abstraction -- because all human concepts are approximations, useful fictions, as application to reality. (They can be very useful fictions, yet none the less all thinking is abstraction of some form, and all thinking gives only an approximation of reality and is not the reality itself.) (Note there are philosophical positions that differ, but I am speaking of the way of science where we make rudimentary “naïve” philosophical assumptions about there existing a physical reality that can be experienced in common, and that is the subject of the foregoing discussion of “reality”.)
So if “interpretive” perspective is descriptive of how the terms are being used when “information” terms are being used in biology, then I claim that this is what is meant when these terms are used -- that the writers of papers that use abstractions from information theory are using meanings that are very close if not exactly in conformance with my “interpretive” perspective. As such this is highly relevant to the issue of whether there is physical evidence to differentiate certain views of reality. (In other words to distinguish propositions or hypothesis of the physical nature of physical reality, of nature.)
I think that part of the issue of the relevance of “information” theory terminology is whether there is good reason to expect such terminology to be applicable to systems that arise by natural means like evolutionary processes. (Including processes under investigation in OOL research.)
The reason is that we have a simpler explanation if information processing terms can be reasonably applied to processes that happen across the board including such cases as evolutionary processes and other natural processes. Now mike has made distinctions between evolutionary and other processes in the literature, and notes that such terms are used less frequently in literature such as geology.
My point about “interpretation” is not directed to the issue of our interpretation of evidence, rather is directed to the very definition of “information”. If what we find in biological systems is that “information” is what occurs when systems “interpret” messages, then we actually find a condition that is only present in a matter of degree that is different in biology than in other systems. Since this is only a matter of degree, there is no discontinuity (as was suggested by Mike Gene) in the biological systems and other systems of nature, beyond this matter of degree.
I am fully accepting that biological systems have processes that are described by information terminology to a greater degree. I am not accepting, based on any evidence that I have observed so far, that there is a hard qualitative difference that is not a matter of the degree. And since these structures can have come about by natural processes we need further evidence to distinguish from more complex natural processes like an agent that is intelligent intervening in their development. So I don’t find the presence of such descriptions, only applicable in a matter of degree, to provide any evidence for the proposition of an agent acting in the sequence of events of evolution.
A definition of information that makes an artificial distinction “designed” to produce a particular conclusion cannot be supported on its own, but rather requires additional evidence. Thus I don’t find that Mike’s method has “probing power” because it does not so far have any description that distinguishes the hypothesized cases by way of observing physical evidence. In other words if both intelligent agents acting, and natural processes not involving natural agents would both produce information processes as observed, there has been no distinction made by observation of physical nature. Mike’s “hunch” is very interesting -- now we need to develop evidence to distinguish mike’s hunch from other hunches like the hunches of all the OOL researchers. The OOL researchers have some evidence to back up their hunches, incomplete as it is, for example. Let’s consider if there is any evidence for Mike’s “hunch”.
quote:
I already mentioned one thing above - 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. This prediction follows from the hypothesis that life is advanced technology. Thus, as our own technology advances, we will better appreciate what is going on inside life.
I make the assumption that biological organisms inherently work by having “messaging” systems that communicate when the physical transport system of communication connects with “interpretation” of those messages by physical systems that react. Thus biological systems are complex systems of stimulus-response, taken in very general terms. As such one can easily predict that “pattern of convergence between biology and technology, to the exclusion of the other physical sciences” because the matter of degree that is present of the detail and complexity of biological systems. So Mike’s “prediction” as far as I can tell predicts that biological systems will be complex. I think I already knew that, and I don’t think it is distinguishing from other hypothesis, for example the OOL hypotheses in OOL research. As such there is no new evidence, no new “probing power”.
[ 22. February 2003, 21:33: Message edited by: gedanken ]
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charlie d.
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posted 22. February 2003 22:50
quote:
I already mentioned one thing above - 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. This prediction follows from the hypothesis that life is advanced technology. Thus, as our own technology advances, we will better appreciate what is going on inside life.
If by this you specifically mean information technology, I do not see see how this is a "distinct" prediction. 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.
It comes to no surprise that information technology terminology and logic, now that it has come to maturity, is being applied to the biological sciences. This is equally true in any conceivable ID-based and/or evolutionary context.
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gedanken
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posted 23. February 2003 13:31
Charlie D’s comments prompted me to do some searching for use of the term “proofreading” in literature of “information theory”, and in general.
The only references I could find to proofreading were of the normal human activity of reading text carefully (by a human agent), and of computer systems that assist with that activity -- with the exception of the specific application to biology of processes that were called “proofreading”. (The time I spent searching was limited to about an hour or two, so I could have missed many possibilities, and I invite Mike to present links to papers on “proofreading” as part of information theory or communications theory that are not biological application.)
Now Mike’s point seems to be that there is a lot of terminology used in biology comes from communications and information theory. And as Charlie D noted, “proofreading” would come from general terminology of human communication -- but is it part of communication or information theory? Because if it is not, then the use of the term in biology does not represent the kind of extremely significant parallel that Mike seems to be suggesting.
In that context, I wanted to give more detail on my concept of “data becomes information when it is interpreted”, and of the concept that human abstractions are not the physical reality that is modeled. These bear highly on the relevance of the analogy to information theory, in my opinion.
Abstraction is not the physical entity
RBH is exactly right about one of my points when he says:
quote:
As I read it, that means that the notion of abstract "information" existing independently of a physical instantiation or manifestation is a description of (i.e., is about) physical systems but is not in itself some sort of entity or causal force. This line of argument is parallel to that of the late Rolf Landauer, who argued that information could not be understood independent of (in isolation from) its physical embodiment.
The notes on Landauer are well worth reading.
The point of this aspect is that since the notions of information processing are not independent of the physical systems that do the processing, that the abstractions of those processes are not independent of the physical processes of the development of those processes themselves. In other words we have very significant concepts of how such processes themselves develop over time, e.g. by evolutionary mechanisms. As such, analogies of abstractions really have no value as evidence for commonality of causation, because they do not provide any link to the causal history of those processes.
Yet all of our “models” of reality are mental abstractions, and they are necessarily imperfect. The point is that to get an accurate mental abstraction of “information”, one has to refer the mental model to the physical embodiment in which it occurs, the mental model has to encompass enough of the relationships of. the physical system being studied to have meaningful relationships.
I hope I am conveying that all concepts are mental models in some level (all imperfect), and that to make them useful one has to do the best possible in grounding them in the physical world experience. This is the essence of science.
Data becomes information when it is interpreted.
This is a view or partial definition of information itself. It is a concept of an abstraction. In other words, in the terms of the last section, I am examining our abstract models of physical reality and then trying to determine a more refined definition of “information” as applied within those abstractions.
“Data” and “information”, as Landauer suggests, must be embodied in a physical form and cannot be understood independent of (in isolation from) its physical embodiment. But how do we distinguish (in our abstractions of that physical reality) when a physical embodiment of energy is just some more physical entity, and when it fits the pattern that we will call “information” (in our abstraction)?
In the concept that I am describing, data can come from anywhere and in any physical form. A stream of noise in a (physical) electrical communication channel is “data”. The momentum of a rock (unmeasured) can be considered as “data”. (And aggregates of such aspects, rather than single aspects, are really what I am referring to as “data”, as data normally is considered as an organized set of multiple aspects and not a single “data point”.)
Now let me recursively apply the concept of a mental model of the human having a mental model. (This must be a “model” because I am trying to maintain the distinction of the first section that mental models are approximations to reality and are not reality itself.) In this concept (within the model now) the human receives energy which stimulates the human nervous system in various forms. We shall call all such energy of stimulation “data”. But when the human reacts by “interpreting” the data in some form, then the “data” becomes “information” (thus partially defining “information”).
This is where we relate Shapiro’s points to the model of physical reality of biological systems, and this (partial) definition of “information”.
Shapiro shares Daniel Dennett’s mistake. Dennett over-characterizes possibilities for artificial intelligence as problems of “computation”, for example. He denies possibilities for artificial intelligent systems performing at human-like levels because he insists that the very processes of “modeling” that I was speaking of in the last section must be done by strict symbolic computational means. This ignores the human ability to do approximate reasoning, and that such approximate reasoning could be accomplished by physical systems. But systems that can do approximate reasoning get past limitations (such as computability) by ignoring them, and by finding approaches first in analogy-related manner rather than strict logical argument. Concepts such as identified by Dennett (such as the “frame problem”) are not inherently non-computable, simply because they will not be solved by the strict methods of symbolic computation that has inherent limitations, but rather will be solved by approximate reasoning that is successively refined.
Data (or stimulus) becomes “information” when it is interpreted by a physical system. But what does “interpret” mean? That is something that must also be dealt with by approximate reasoning, as there is no hard and fast, totally objective and mechanically determinable rule for what is “interpretation”. In fact “interpretation” is a matter of degree, when we observe a complex system process complex stimuli we agree that it is “interpreting” the data. When we see a simple system reacting, we are less able to make that identification. But it is the point of approximate reasoning that this is a matter of degree.
We don’t seem to think in terms of one rock in space hitting another and causing the second rock to “respond” according to the relationships of physics as a serious case of “interpretation”. I claim this is a matter of degree. For when a complex biomolecular system sends a chemical “message” that is processed by a receptor, it is considered “communication”, and thus the receptor is “interpreting” the message or data transported by the physical transport system. But these are not cases of a complex human thinking process interpreting the data, but of (relatively) simple and understandable biomolecular processes acting on the strict physical level. They are not distinct from the pool ball or rocks striking according to relationships of physics, except in a matter of degree.
But I could use the terminology of a “feedforward” control system to describe what happens when I sink a pool ball by striking it with a que ball. The “feedforward” action occurs without feedback at that point, and is only considered a “control” action because it was preceded by my action. But is it, or is it simply the stimulus-response that makes it a “feedforward” system? This is strictly a matter of degree, and there is no hard fast rule for differentiating when stimulus or “data” becomes “interpreted”.
Likewise Mike Gene shares Shapiro and Dennett’s mistake in over-emphasizing the analogic relationship of “information” (or communication) while missing out on the very point of the fuzzy or approximate nature of analogic reasoning. To relate back to causal history, one must examine the details of the underlying physical systems in reality, and relate our causal models to that physical detail and not to high-level abstractions. The mistake is trusting this “analogic” style reasoning, without recognizing how the very notion applies in observation of these communication and information systems themselves.
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Mike Gene
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posted 23. February 2003 15:27
RBH: In A 21st Century View of evolution on his web page Shapiro identifies his approach as non-Darwinian. (Parenthetically, it's not altogether clear what Shapiro means by "Darwinian" but the implicit meaning, given his off-hand remarks in several papers, seems to be gradualist-one-mutation-at-a-time-little-bitty-steps-incrementalism, sort of like the caricature of Dawkins' position one often sees.) Whatever his conception of "Darwinian," it is clear that he believes that the natural genetic engineering toolbox he writes of is non-Darwinian. The question that interests me, though, is whether the tools themselves could have arisen in Darwinian fashion.
A more significant question, IMO, is whether the tools themselves did arise in Darwinian fashion. Establishing that they "could have" puts the skeptic in the position of proving the impossible (i.e., they could not possibly have arisen in Darwinian fashion).
However, I don't think it fair to portray Shapiro as employing a "caricature of Dawkins' position." Many scientists seem to equate darwinism with "gradualist-one-mutation-at-a-time-little-bitty-steps-incrementalism."
For example, DavidFaguy writes:
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Many scientists now believe that microbes change so much (by non-Darwinian mechanisms such as lateral or horizontal gene transfer) that it may be ridiculus to try to reconstruct a phylogeny.
Then there is this
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Prokaryotes are profoundly original, highly efficient microorganisms that have played a decisive role in the evolution of life on Earth. Although disjunct, taken together their cells form one global superorganism or biological system. One of the results of their non-Darwinian evolution has been the development of enormous diversity and bio-energetic variety. Prokaryotic cells possess standardized mechanisms for easy gene exchanges (lateral gene transfer) and they can behave like receiving and broadcasting stations for genetic material. Ultimately, the result is a global communication system based on the prokaryotic hereditary patrimony, by analogy, a two-billion-year-old world wide web for their benefit.
Perhaps it would help if we broadened our perspective and consider how Kimura's Neutral Theory mixes with neo-Darwinism.
Gert Korthof entitles his review of Kimura's Neutral Theory such that this theory is an "attack" on neo-Darwinism. Korthof writes:
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Kimura's 'Neutral Theory' got a firm place in the standard textbooks on evolution and population genetics, despite being clearly anti-selectionist. In the beginning orthodox Darwinists did not exactly like Kimura's theory, because he was telling the scientific community that all-powerful Natural Selection was not so powerful after all. Natural selection had its limitations. On the molecular level the power of Natural Selection was greatly minimised, if not banished at all. Randomness took its place. Molecular variation in proteins and DNA was uncovered that had no influence on the fitness of the individual organism: in other words: is selectively neutral. One could even doubt if Natural Selection was of any importance in the traditional areas of morphology and anatomy. - emphasis added
Let me expand on this by providing a very helpful (and lengthy) excerpt from Masatoshi Nei's "Molecular Evolution Genetics" (Columbia University Press; 1987). He puts it better than I could:
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The term neo-Darwinism has been used to represent various versions of modified Darwinism since the late nineteenth century, but at the present time it usually means the evolutionary theory formulated by Fisher (1930), Wright (1931), and Haldane (1932). In the 1920s and 1930s, these three authors conducted extensive mathematical studies on the change in gene frequencies due to mutation, selection, and genetic drift and reached the conclusion that selection is much more effective in changing gene frequencies than mutation. This theoretical work was soon accepted by a number of leading experimental geneticists, notably Dobzhansky (1937), who wrote an influential book on evolution entitled Genetics and the Origin of Specied. Through this book, neo-Darwinism was gradually disseminated among biologists, and various authors (Dobzhansky 1937, 1952; Muller 1940; Simpson 1944, 1949, 1953; Huxley 1942; Mayr 1942, 1963; Stebbins 1950; Ford 1964) made further refinements of the theory. Because of these works, neo-Darwinism was accepted by most biologists by 1960.
Following King (1972), we can characterize neo-Darwinism by the following statements [see Dobzhansky (1951, 1970), Simpson (1953), and Mayr (1963) for details].
1. Mutation is random with respect to gene function and recurs with reasonable high frequency.
2. Mutation is the primary source of variation, but its effects on gene frequency change is so small that is plays a minor role in evolution.
3. Because of mutations that have occurred in the past, natural populations contain sufficient genetic variability to respond to almost any kind of selection.
4. Evolution is determined mainly by environmental changes and natural selection. Since there is enough genetic variability, no new mutations are required for a population to evolve in response to environmental change. There is no relationship between the rate of mutation and the rate of evolutionary change.
5. Because mutations tend to recur at reasonably high frequencies, the majority of clearly advantageous mutations should have been fixed or should have reached their optimum frequencies in the population. Therefore, the genetic structure of a population is almost always at or near its optimum for a given environment.
6. Evolutionary change of a species occurs gradually by means of natural selection. Thus, macroevolution is nothing but the accumulation of the effects of microevolution.
<Nei then goes on first list some of the different points of emphasis among the neo-Darwinists and then turns the experimental observations at the molecular level. After providing a list of seven findings, he writes the following:- MG>
The first two properties of molecular evolution were recognized as soon as Zuckerkandl and Pauling (1965) and Morgoliash and Smith (1965) started extensive studies on the evolutionary changes of hemoglobin and cytochrome c. They tried to explain these observations in terms of neo-Darwinism. For example, Morgoliash and Smith thought that a constant rate of amino acid substitution per site per year is possible if various types of selection are averaged out. For these biochemists and even evolutionists such as Simpson (1964) and Mayr (1965), the idea of fixation of a mutant gene in a large population without the aid of natural selection was unthinkable at the time.
A careful examination of the first two properties of molecular evolution, however, indicates that they contradict most of the principles of neo-Darwinism mentioned earlier. In neo-Darwinism, the rate of evolution should depend on how often and how fast the environment changes. Thus, we would expect that the rate of evolution in living fossils such as the lamprey is much slower than that in rapidly evolving groups such as the primates. In reality, however, the hemoglobin in living fossils seem to have evolved nearly at the same rate as those of the primates (Jukes 1971). According to neo-Darwinism, the rate of evolution should also depend on population size and generation time (chapter 13). As we have already discussed, this prediction does not hold for molecular evolution. Similarly, the observation that functionally less important genes or parts of genes evolve faster than functionally more important ones is incompatible with neo-Darwinism. In neo-Darwinism, most gene substitutions are supposed to occur by positive Darwinian selection, and thus functionally important genes or parts of genes are expected to show a higher rate of evolutionary change than functionally less important ones (chapter 4 and 13).
It is also difficult to explain both the level of protein or DNA polymorphism and the rate of nucleotide substitution with a mathematical model based on neo-Darwinism (chapter 8 and 10). Furthermore, the genomes of higher organisms are quite flexible and subject to rather rapid structural change without much phenotypic effect (chapter 6). - emphasis added
Thus, it would seem to me that Shapiro is simply working with the definition of "Darwinian" that was developed by Darwinian scientists.
As for what Shapiro means by non-Darwinian evolution, you should have asked when he held the chat session. I suspect it boils down to the notion that evolution is more internally driven than we realize. For example, elsewhere, he introduces a conference where views similar to his were proposed as follows: the debate moved toward thinking of "evolution as biological function" rather than of evolution as accidental changes captured by selection.
Evolution "as a biological function" is different that evolution as accidental changes captured by selection. Put simply, Shapiro is making evolution more biological.
Secondly, as with neutralists, Shapiro is advocating a view where natural selection is kicked off its throne. It no longer acts as the busy-body overseer who monitors each step of the design, but instead simply gets called upon for final approval when the intracellular designers are finished.
Then again, perhaps the Darwinists themselves should define 'darwinian.' There seems to be a general backing off from the concepts of gradualism, competition, and the ubiquitous/essential role of selection. The Modern Synthesis, as described by Nei, has been quietly taken off the table.
As Arlin Stoltzfus puts it:
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Thus, while there are clearly common threads linking past and present thought in evolutionary biology, the evolutionary theory of today is not that of Darwin, nor even that of Darwin's mid-20th-century successors. This yet-to-be-named new view, with its empirical emphasis on rates and patterns of divergence, and its reliance on, not only natural selection, but also mutation biases and developmental constraints as causes of non-randomness in evolution, has already enjoyed considerable success.
Or as Jazz put it on ARN:
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Every controversial aspect of evolutionary thought will have a Darwinist position. In self-organization, it's the functionalists vs. the structuralists. In evo-devo, it's the externalists vs. the internalists. They are the gradualists vs. the punk-eekers, and the adaptationists vs. the neutralists. Darwinists may not come out on the winning side of these controversies, as with LGT and endosymbiosis. But the Darwinist philosophy perseveres by the adjustment of understanding, and the accommodation of new developments. Again, I give Darwinists credit for this. As long as it's clear to everyone that Darwinism is an overriding philosophy and not a concrete position, I have no problem with this.
[ 23. February 2003, 15:28: Message edited by: Mike Gene ]
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Mike Gene
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posted 23. February 2003 15:30
Gedanken: My point about “interpretation” is not directed to the issue of our interpretation of evidence, rather is directed to the very definition of “information”.
I understood this. I was just trying to highlight another point I have been making for years, since your point conveniently underscored it. Anything we consider as "evidence" is also "information." Thus, the inherently subjective nature of "evidence." This is relevant given your requests for "evidence" below.
Gedanken: But this gets back to my point that such concepts are abstractions of what the biological system really does.
Sure. And when something is designed, what the physical system really does is act as a representation of a conceptual abstraction.
Abstract models are creations of human intelligence, and are not the actual workings of the biological organism.
That's just one interpretation. A design theorist considers the possibility that such abstract models are "connecting" to another mind's abstract models. The physical system is simply a medium of "communication," being a representation of another mind's conceptual world. Not too much different from our communication using this technology at the moment.
So my suggestion is that “proofreading” is actually a physical process that reminds the human in abstraction of proofreading a text.
Indeed. That's why Davies' point comes to mind - "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)."
I don’t think that there is any absolute meaning in abstraction -- because all human concepts are approximations, useful fictions, as application to reality.
If we are dealing with advanced design, then yes, our abstractions, being rooted in primitive design, may amount to only useful fictions. Nevertheless, we would expect our design concepts to be the most useful fictions. And that's what we see. And as our own designs improve, we might expect to move beyond useful fictions and make real connections between the abstract worlds inhabited by mind.
So if “interpretive” perspective is descriptive of how the terms are being used when “information” terms are being used in biology, then I claim that this is what is meant when these terms are used -- that the writers of papers that use abstractions from information theory are using meanings that are very close if not exactly in conformance with my “interpretive” perspective. As such this is highly relevant to the issue of whether there is physical evidence to differentiate certain views of reality.
What's most relevant at this point is whether a design approach can develop a track record of experimental success. After this is accomplished, it may be worth considering how much we can tease apart these alternative perspectives. But it doesn't make sense to ask design proponents to come up with such "physical evidence" (which, as we see above, involves subjectivity) before they have matured their perspective.
If what we find in biological systems is that “information” is what occurs when systems “interpret” messages, then we actually find a condition that is only present in a matter of degree that is different in biology than in other systems. Since this is only a matter of degree, there is no discontinuity (as was suggested by Mike Gene) in the biological systems and other systems of nature, beyond this matter of degree.
This is an important point. According to the argument Gedanken is offering, there is only a difference in degree between human technology (things known to be designed) and the other systems of nature also. And this would suggest that the residue of design is not necessarily traced to some "discontinuity." Detection of design may be much more subtle.
I think there are two important points of distinction that come into play. Again, this appears to be an issue of what I call ontological evidence and epistemological evidence. While a complete discontinuity with the physical sciences would be a good way to convince a skeptic of ID, I'm not sure that such a thing follows from the truth of design.
Secondly, when we get through all the fancy terminology and concepts both sides argue about, it boils down to gestalt shift - are we reading teleology into non-teleological phenomena or are we giving teleological phenomena a non-teleological interpretation? As such, folks like Gedanken are rightly worried about false positives. But just as rightly, folks such as I are worried about false negatives. No one has found that sliver of insight where the concern for false positives and false negatives is balanced out to the satisfaction of all. Yet one should not paralyze an ID investigation waiting for this moment of consensus.
I am fully accepting that biological systems have processes that are described by information terminology to a greater degree. I am not accepting, based on any evidence that I have observed so far, that there is a hard qualitative difference that is not a matter of the degree.
But here the two major assumptions come into play again. First, expecting a "hard qualitative difference" does not necessarily follow from design. In biology, the two hybrid system employed in yeast is designed. Yet there is no "hard qualitative difference" between it and other biological processes. Thus, it would be nice, for the sake of consensus, to find such differences. But no design theorist should hold their research hostage to such a sociological state.
Secondly, again it's about "evidence" Gedanken has "observed so far." But evidence is interpreted data. "Evidence" is abstraction, approximations, useful fictions, as it applies to reality. I can hardly be expected to wait for Gedanken's permission before proceeding.
The point that matters is that we agree that "that biological systems have processes that are described by information terminology to a greater degree." And it's not just information terminology, but engineering terminology. Put simply, it's technological terminology that exists as a consequence of minds trying to smartly shape reality. Now, Gedanken needs more before taking ID seriously. That is his epistemic right, which is why I have never demanded that he, or anyone else like him, subscribe to my views. But I don't need more to run a research program. We need to tease apart the establishment of a research program and the ability to generate widespread consensus, as they are not the same thing.
And since these structures can have come about by natural processes we need further evidence to distinguish from more complex natural processes like an agent that is intelligent intervening in their development. So I don’t find the presence of such descriptions, only applicable in a matter of degree, to provide any evidence for the proposition of an agent acting in the sequence of events of evolution.
Fine. What is interpreted as evidence is always open to reinterpretation. The point that matters is that the hypothesis of an intelligent agency intervening in history can be mapped out in an experimental fashion. The fact that biology, like engineering, and unlike other fields of science, is so deeply indebted to technological concepts can be used to support and guide the hypothesis of life's design. If I were trying to go beyond an investigative hypothesis and instead cite such dynamics as some sort of proof (or evidence that demands consent), you'd have a point. But one is under no intellectual obligation to jettison a design inference because it's possible to interpret teleological phenomena in non-teleological ways.
A definition of information that makes an artificial distinction “designed” to produce a particular conclusion cannot be supported on its own, but rather requires additional evidence. Thus I don’t find that Mike’s method has “probing power” because it does not so far have any description that distinguishes the hypothesized cases by way of observing physical evidence.
The probing power comes with its ability to probe nature, not settle debates. The fact remains that the hypothesis that life was designed provided the probing power to detect the relationship between cytosine deamination and protein evolution in a manner that begins to put flesh out the hypothesis of front-loaded evolution. If I were to spend all my time trying to establish a "discontinuity" to satisfy the skeptics, I wouldn't have noticed this relationship and thus begun to flesh out ID in a positive manner. I have taken the demands for a positive expression of ID seriously.
In other words if both intelligent agents acting, and natural processes not involving natural agents would both produce information processes as observed, there has been no distinction made by observation of physical nature.
Thus, ambiguity continues to allow room for alternative perspectives. It might be helpful to consider things from my perspective. That is, while you might take notice that I have failed to find something that converts you (and others) to ID, I take notice that you and the entire global scientific community have failed to rule out ID (thus providing the impetus for me to abandon ID). Now, given that more and more, universal life features cluster with technology, to the exclusion of other natural processes, and the hypothesis of ID has never been ruled out, the ID hypothesis is worth exploring. The remaining key is whether such hypotheses bear fruit. And I would submit that I have shown they do, even at this very early and rudimentary level. Not enough for a clean-cut distinction? Doesn't matter.
Mike’s “hunch” is very interesting -- now we need to develop evidence to distinguish mike’s hunch from other hunches like the hunches of all the OOL researchers. The OOL researchers have some evidence to back up their hunches, incomplete as it is, for example. Let’s consider if there is any evidence for Mike’s “hunch”.
Yes, appealing to OOL research is key. First, as I suggested otherwise, my hypothesis about design is tied to the OOL on this planet. Thus, it only makes sense to apply the same standards that are applied to current work regarding OOL. See this. Thus, the inability to come up with clear-cut hard distinction is simply not important at this point.
Secondly, as far as the evidence that backs up traditional OOL hunches, we must keep in mind the context of this research. Clas Blomberg, a researcher of abiogenesis, writes that origin of life research "is aimed to show how it could have happened"(emphasis added/ J Ther Biol 187:541-554). And when it is time to evaluate various speculations about the origin of life, Blomberg points out that the "primary question is not: "is this the way it happened?", but rather, "what arguments support the possibility that it could have occurred this way and what speaks against it?" Thus, we must remember that the evidence supporting OOL hunches does not work to establish that the Earth did indeed spawn Life. It amounts to circumstantial evidence that supports speculations about how something might have happened. Scientists do not have a hunch that the Earth spawned Life. The begin their analysis with this belief. It's more of an assumption than a hunch. Now, that we can agree that life is technology allows design theorists to learn from this approach and speculate, for example, about the purpose of this technology and how it plays out. The research becomes "what arguments support the possibility that life could have been designed to carry out X and what speaks against it?" Etc.
Thirdly, keep in mind also that OOL research has never ruled out the design of life. That is, a competing hypothesis was not eliminated prior to investigating the chosen hypothesis. And the manner in which the chosen hypothesis is being fleshed out doesn't feed back onto the original question and thus doesn't hold any promise of ruling out design.
I make the assumption that biological organisms inherently work by having “messaging” systems that communicate when the physical transport system of communication connects with “interpretation” of those messages by physical systems that react. Thus biological systems are complex systems of stimulus-response, taken in very general terms.
A view that comfortably fits into a design perspective. As I mentioned above, ID survived an important test of falsification. Present day biology is much more ID-friendly than it was a few decades ago. In fact, that's why I take ID seriously.
As such one can easily predict that “pattern of convergence between biology and technology, to the exclusion of the other physical sciences” because the matter of degree that is present of the detail and complexity of biological systems. So Mike’s “prediction” as far as I can tell predicts that biological systems will be complex.
I don't think it's an issue of complexity. For example, I'm not sure the lac operon is much more complex than a tornado. Or even the galaxy itself. Yet I don't see where concepts such as translation, error-correction, and checkpoints come into play when trying to understand tornadoes and our galaxy. Furthermore, as I mentioned above, while mammals are probably more complex than bacteria, I don't know of any technological concept that applies only to mammals. For example, you'd probably have a better case if we only saw proofreading and machines in mammals.
My prediction stems from the hypothesis that we're dealing with advanced technology. As nobody pointed out above, "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." The hypothesis of life's design predicts that what is needed to fully grasp life is a knowledge base that stems from understanding technology. That concepts from our own technology shed light on biology is exactly what we would expect if ID were true.
Furthermore, it's not just an understanding of life that depends on knowledge of technology. I predict the same point will extend to evolution. A couple of years ago, I offered the following:
The non-teleological view of evolution is that it is not really a biological process, but instead is the consequence of many smaller biological processes. Or look at it this way: the purpose of life is not to evolve; it just happens. But a teleological view of evolution likens it to a biotic process (roughly analogous to ontogeny). Evolution was intended/anticipated. I suspect much of the so-called junk DNA comes into play here. Is evolution really nothing more than a by-product of messy molecular interactions or is it far more sophisticated (itself being designed)? Concerning the cell and its contents, Bruce Alberts noted, " But, as it turns out, we can walk and we can talk because the chemistry that makes life possible is much more elaborate and sophisticated than anything we students had ever considered. " More and more, I am coming to seriously think that in another few decades, another leading scientist will write, " But, as it turns out, we exist because evolution has been much more elaborate and sophisticated than anything we students had ever considered. "
When we consider it is becoming increasingly clear that the Modern Synthesis fails to capture important elements of evolution, and the view of evolution that Shapiro and others are beginning to elaborate, it would seem that my prediction is on track.
I think I already knew that, and I don’t think it is distinguishing from other hypothesis, for example the OOL hypotheses in OOL research.
And how have OOL hypotheses distinguished themselves from my hypothesis of life's design? Y'see, this doesn't matter that much, now does it? All that matters is that we seem to be reaching a consensus that life is technology. And surely you must realize that a view where cells are computation devices that may control much of their own evolution is not a view that is inconsistent with or hostile to ID.
As such there is no new evidence, no new “probing power”.
Sure there is. This is just the beginning.
[ 23. February 2003, 15:36: Message edited by: Mike Gene ]
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Mesk
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posted 23. February 2003 23:45
quote:
Mike Gene:
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.
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nobody:
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.
These sort of conferences are in fact happening all the time, as anyone currently working in the biological sciences would be aware. The analysis of previously unimaginable quantities of raw data obtained from modern genetic and molecular biological research - in other words, the emerging field known as bioinformatics - is forcing biologists into close collaborations with computer scientists, mathematicians and statisticians. In the past two years I have attended probably half a dozen seminars and conferences explicitly designed to foster cooperation between biologists and computer/information scientists.
Such meetings have been, to a greater or lesser extent depending on the participants, quite valuable in furthering the tools available for mining biological information. What they have not been (at least as far as I can tell) is fora for the mass conversion of scientists to belief in ID. Rather, some of the most successful advances in bioinformatics have involved an explicitly evolutionary approach to analysing biological data - for instance, methods for assessing the potential disease relevance of genetic polymorphisms by taking evolutionary conservation into account, or for identifying important loci in humans and experimental organisms by looking for the "molecular signature" of natural selection. Many other new bioinformatic techniques, most notably tools for phylogenetic analysis and identification of molecular traces of evolution and demographic history, are designed to explore predictions made by evolutionary science.
The merging of biology and computer science predicted by Mike Gene is already occurring. I have seen no evidence, however, that this has resulted in a paradigm shift amongst biologists towards ID.
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nobody:
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.
In this thread, Mike Gene and others have shown convincingly what most biologists already know - that life is in many ways "computer-like." What is thus far lacking is any compelling reason to believe that this is in fact evidence for intelligent design. IMO, evolutionary processes are just as capable of generating efficient information-processing machines as intelligent design.
It is not enough for IDists to point to aspects of biological organisms which resemble manmade systems and proclaim these to be evidence of design. They must also provide evidence that such features are somehow better explained by intelligent design than by modern evolutionary theory. The IDists posting in this thread appear to be ignoring an alternate, and eminently plausible, hypothesis - that features of biological organisms resemble those of manmade devices because these features are optimal for any information-processing system, and have thus been favoured by natural selection over evolutionary time. Similarity between biological and designed systems could easily represent fundamental functional constraints resolved in the same way by both evolutionary processes and intelligent designers.
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