Best Possible World: Gateway to the Millennium and Eschaton

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There are many now, and will be many more in the months ahead, who, when asked, will say that I am beating an already dead horse. They may be correct. Perhaps I should be speaking of materialism's wake. It will be more like a party, really a celebration, as all good wakes are supposed to be (see, again, Finnegans Wake -- talk about prophetic, I'm just the amateur in this neck of the woods).
This will be a universal wake. Attendance, nay, participation will be virtually mandatory. I will not be the party-pooper. This time I will be the party-planner. Just recall that this is the before-party. We are talking pre-millennialism. I am the wedding planner. I'm the Hierogamos guy. The Columbia crew got to celebrate their nuptials just about a thousand years early, those lucky stiffs. The Heaven's Gaters don't really count: they were party crashers; although, on second thought, and to be perfectly honest, I was standing at that gate.
How exactly will the 'Ome explosion' subvert the epistemic-ontic divide? Without a central theory of complexity, without a Grand Unified Theory of complexity, there can be no coherence in the mushrooming Omic fields. There will be no single measure of complexity -- no single definition of it. Complexity will necessarily be an ad hoc science, a pragmatic science. Complexity will have to be defined in terms of ad hoc, pragmatic and functional considerations. These consideration are all strongly subjective in nature. The now exploding science of complexity will be the first objectless science. Epistemology and ontology will be officially reintegrated.
Is not psychology already an objectless science? Yes, but just for that reason, most scientists did not consider it to be scientific. But now with biology teetering on the brink of objectlessness, with the entire medical system hanging in the balance, the scientific establishment is going to have to do a public soul-searching concerning the nature of science. Just when it seemed that the biological sciences were poised to switch from 'soft' to 'hard' science, the ontological rug has been pulled out from under them by the 'Ome explosion'. As biology slides back into the softness of the soft sciences, it will threaten to pull the rest of science with it. There will be last-ditch resistance from the hard-core scientists. The (Sokal) 'Science Wars' will re-ignite. This time the hard-core objectivists will find that their end of the stick will be much shorter than it was just a few years ago. Thus will end objectivism and the epistemic-ontic divide.

On complexity and emergence -- Standish, R. K.

Numerous definitions for complexity have been proposed over the last half century, with little consensus achieved on how to use the term. A definition of complexity is supplied here that is closely related to the Kolmogorov Complexity and Shannon Entropy measures widely used as complexity measures, yet addresses a number of concerns raised against these measures. However, the price of doing this is to introduce context dependence into the definition of complexity. It is argued that such context dependence is an inherent property of complexity, and related concepts such as entropy and emergence. Scientists are uncomfortable with such context dependence, which smacks of subjectivity, and this is perhaps the reason why little agreement has been found on the meaning of these terms.

How much complexity is too much for biology? That depends on how much can be explained.

There will only ever be one natural explanation for biological complexity: natural selection. How great is the explanatory burden which natural selection can bear? The good news is that we do not know the limit. The bad news is that we do not know the limit. In other words, we have no idea as to the explanatory power of natural selection. The saving mantra of the naturalists is that there is no alternative explanation. How long can they maintain this stance in the face of the explosion of complexity? I guess we'll find out. So far, they are putting a brave face on it -- keeping a stiff upper lip.
Occasionally it is suggested that natural selection can explain virtually no complexity. How often do the naturalists have to remind us that there is no direction to evolution? They readily admit that there is nothing in natural selection to suggest a secular or temporal increase in complexity. Complexity is not a trait, per se, which would ever be selected for. Complexity might augment adaptation, or it might not, depending on the particular circumstances. This is just another aspect of the objectlessness of complexity. The objectlessness of traits is another matter.
Certainly in engineering it is simplicity that is golden. There was an overriding imperative to simplify the functional designs of our artifacts until, it would seem, we came to the computer age. There has, subsequently, been an explosion of complexity that is frequently compared with biological complexity. Does this artificial complexity provide any explanation for its biological counterpart? It hardly seems so. In fact, it is just the 'bioinformatics' (992,000 hits) being made possible by computers that is mainly responsible for our exploding awareness of biological complexity.
Is there a biological limit to complexity? Is there any way to predict how much more complexity we may be discovering? Will our ability to discover biological complexity be limited only by epistemology? Were any biologists ten years ago predicting the explosion of complexity we have witnessed in the past ten years? I seriously doubt it.
Was there not a general impression among biologists that biological complexity must be limited by the amount of information that is contained in the genetic code? What has happened to this notion? Is the current explosion not seriously threatening any such limitation or linkage, if it has not already overrun it? Is there not emerging a very serious information gap between the cell and the gene?
It will be more than curious to watch the impact of the biological complexity explosion on Artificial Intelligence. It is now requiring supercomputing power simply to delve into the complexity of just few aspects of a single cell. Where does that leave us with regard to simulating the the brain power of the interactions of 10^11 of such cells? Does this not foreshadow an indefinitely widening gap between natural and artificial intelligence, just when the pundits were predicting that we were on the brink of having our carbon rendered obsolete by silicon.
Nowhere is the genetic information gap greater than when it comes to explaining biological or natural intelligence. One can almost do the calculation on the genetic side. The human genome carries less than 40,000 functional genes, with an average of 72,000 base pairs each, and they are >~99% identical to those of chimpanzees. The difference in native intelligence between the chimps and us is to be explained by no more than something on the order of a megabyte of code. Imagine that! When I last checked, Windows XP was 500 megabytes. Are to we believe that blind and random natural selection is so much more efficient and direct than 30,000 Micro-softies hammering diligently at their keyboards? And besides, at every conception of a new human, how much of that one megabyte total for our IQ code is being randomly scrambled by the natural process of genetic recombination? Imagine what would happen if we were to randomly recombine my binary code for XP Home with my wife's binary code for XP Professional (Library Edition). What would be the IQ of the resulting mish-mash? I think our son would have been institutionalized long ago.
This is hardly rocket science, is it? But where else on the Internet is anyone keeping score for materialism and naturalism? The only other articulate skeptics are the Intelligent Designers. But they are much more mechanically minded, in their very narrow pursuit of Design, than even are their naturalist opponents. They are more genetically minded even than the geneticists. Their view of Creation is every bit as clunky as that of the UFO-nauts with their alien breeding stories. For the Creationists, the notion of vitalism is as welcome as Witchcraft. (Forget Harry Potter!) Their God is the one painted on the ceiling of the Sistine Chapel, and they don't even have the gender right!
There is a stonewall of silence when it comes to a holistic and substantive critique of the Scientific worldview. That barrier of silence will be broken, right here on the Internet.
There is an apparent information gap between the genes and the rest of biology. This is not unlike the 'missing mass' or the 'dark matter' that is believed to comprise almost ten times as much mass as the visible matter in the universe. In biology we have missing information. Where is it? Is it in the genome, the proteome, the metabolome, etc.? It is manifested in all of these places, but resides in none of them. Consider how much information is contained in all the laws of physics. Where does that information reside? Certainly not in each one of the elementary particles. Like organisms, the elementary particles exhibit many law-like traits, but we do not suppose that these traits are coded in their genes. It may be that the genetic information simply serves to trigger and amplify an information that is much less particulate or even physical.
It may well be that there is holistic, informational 'mind' field. It may have holistic properties rather like language. The eight letters of the word 'elephant' certainly do not contain all of the information of the word. The information is to be found in the relational properties or associations of that word with all the other words of the language. Thus it is with genes and proteins, etc.
What about the Mandelbrot set? How much information is contained therein? It would naively appear to be infinitely complex, and yet it can be generated simply by the formula of its 'genetic' kernel z' = z^2 + C, which contains, at most, a few bytes of information. Is there not a similar disconnect between the manifest infinite complexity of the Mandelbrot and its simple genetic formula?
I would suggest that the Mandelbrot exhibits the holographic-like complexity of the entire number system. Every number is a holistic construct, having no meaning in isolation. There is only a number field. There is a similar biological field, with a potentially infinite holographic complexity. The genome operates within and upon that field. Unlike the number field, the biological field has teleological properties that are manifested particularly in our mental states as an intentionality.
At this point it is no great stretch to postulate several intimately related fields or manifolds which contain or carry a spectrum of meaning and functional information. These would be the mental, biological, mathematical, and linguistic manifolds. We should not forget the space-time manifold which manifests the symmetries and laws of physics, and which seems closely associated with the mathematical manifold. Each one of these manifolds has its peculiar ontic and epistemic aspects. The quantum, entropy, anthropics, relativity and the directionality of time all seem to conspire to introduce a strongly epistemic quality into the alleged objectivity of the space-time manifold. If we knew the deeper relations between these several manifolds we would hold the keys to the kingdom. We will have plenty of time to work this out.
In the meantime, we only need to appreciate that reintroducing aspects of vitalism into the semiotic flux of biology would be a very natural step when seen in this larger context. The remaining resistance to vitalism is just the death rattle of materialism. Let us respect its senescence while we plan for its wake. Also realizing that the misguided Creationists may, ironically, be the final source of resistance to vitalism. The force will be with them, too.

To underscore that last point consider:

Thorson's methodological naturalism leaves room for teleology in nature, though a teleology that falls short of full intelligent agency.
For Thorson, getting the scientific community to admit the reality of this functional logic and to make that logic a fundamental focus of scientific investigation would constitute the sort of paradigm shift in science with which he would be entirely happy. He sees Michael Behe's work on irreducible complexity as feeding into such a paradigm shift inasmuch as Behe's work shows that a functional logic pervades biology all the way down to the molecular level (below which biology gives way to physics and chemistry). Nonetheless, Thorson is not willing to follow Behe to his conclusion of intelligent design. Why is that?
The problem according to Thorson is that any sort of designing agent responsible for that functional logic in biological systems would be a scientific surrogate for divine agency. Indeed, from a Christian perspective it is hard to see what a designing agent responsible for biological complexity could be other than the Christian God. Intelligent design, if it could be developed as a scientific theory applicable to biology, would thus have immediate theological implications, not the least being that God's handiwork in nature was empirically detectable and therefore not inscrutable.
But this for Thorson is theologically unacceptable. Following Karl Barth and a theological tradition that places a premium on divine inscrutability, it is unacceptable to Thorson that God's agency in the world not be completely shrouded in mystery. In addition to Barth, Thorson cites Austin Farrer, who argued that the metaphysical joint at which divine agency intersects the created world is fundamentally inscrutable. Thorson concludes that "divine agency is essentially mysterious at every level."
I've long ceased to be impressed by claims of divine inscrutability. Whenever I'm confronted with such claims, I invariably recall G. K. Chesterton's epigram, "We don't know enough about the unknown to know that it is unknowable." To be sure, it might serve certain theological interests to keep God, and divine agency in particular, inscrutable. But the claim of divine inscrutability, just as any other controversial claim, needs an argument if it is to be judged in the market of ideas.
I'm going to have to investigate Thorson on my own. His functional teleology seems closer to a rational theism than does Dembski's watchmaking Mechanic. Why Thorson sees functionalism as favoring the inscrutability of God is presently inscrutable to me. Unfortunately, Thorson's article is not yet available on the ASA website.
What I do notice from perusing biological complexity is that the IDers are continuing to rock the scientific boat. Even though their mechanistic conception of creation is wrong, their boat rocking could well create an opening for a more metaphysical view. I do notice some polarization between the IDers and the ASA contingent. The ASA might provide a platform for a less mechanistic account, as they did for Thorson. Their journal is not posted to the web until one year after publication. If they want to participate in the premillennial politics, they will have to be more expeditious than that. However, they probably will not wish to associate with someone with my radical view of spiritual politics. Once again, we'll have to pray to the Google gods!
Here is the latest scoop:
DARWIN AND DESIGN: A debate about the latest defense of intelligent design. -- William A. Dembski and H. Allen Orr (12/02).
The primary attack on Dembski concerns his mystagoguery. I agree with that criticism. Bill will never be able to squeeze any rational coherence out of his Cartesian dualism.
Dembski refers to James Shapiro (Univ. Chicago) associated with ISCID:
The International Society for Complexity, Information, and Design (ISCID) is a cross-disciplinary professional society that investigates complex systems apart from external programmatic constraints like materialism, naturalism, or reductionism.
That sounds promising!
A 21st Century View of Evolution by James A. Shapiro:
Molecular genetics has amply confirmed McClintock’s discovery that living organisms actively reorganize their genomes. It has also supported her view that the genome can "sense danger" and respond accordingly. The recognition of the fundamentally biological nature of genetic change and of cellular potentials for information processing frees our thinking about evolution. In particular, our conceptual formulations are no longer dependent on the operation of stochastic processes. Thus, we can now envision a role for computational inputs and adaptive feedbacks into the evolution of life as a complex system. Indeed, it is possible that we will eventually see such information-processing capabilities as essential to life itself.
Had I not been forewarned, I might have missed Jim's still implicit anti-naturalism. What he may say in private to Bill is another matter.
There is now a burgeoning field of 'evolutionary computing' (27,000 hits). I am not aware of any pervasive anti-naturalist sentiment in this field. Most of the workers seem to feel that they are actually exploiting Darwin, not refuting him. Where Jim and the ISCID part company with this nascent industry needs investigation.
Genome Organization and Reorganization in Evolution: Formatting for Computation and Function by James A. Shapiro (2001):
Molecular discoveries about mechanisms of DNA restructuring show that cells possess the Natural Genetic Engineering functions necessary for evolutionary change by rearranging genomic components and reorganizing system architectures. The concepts of cellular computation and decision-making, genome system architecture, and natural genetic engineering combine to provide a new way of framing evolutionary theories and understanding genome sequence information.
This is a bit more explicit. This seems rather like the functionalism that Dembski was just criticizing in Thorson. Jim continues:
The most profound, and most challenging, new aspect of thinking in a 21st Century fashion about evolution will be the application of information-processing ideas to the emergence of adaptive novelty. A major problem, often cited by religious and other critics of orthodox evolutionary theory, is how to explain the appearance of complex genomic systems encoding sophisticated multicomponent adaptive features. The possibility that computational control of natural genetic engineering functions can provide an answer to the problems of Irreducible Complexity and Intelligent Design deserves to be explored fully. Contrary to the claims of some Creationists, these issues are not scientifically intractable. They require an application of lessons from the fields of artificial intelligence, self-adapting complex systems, and molecular cell biology.
[...] One philosophical question that has proved extraordinarily contentious concerns the respective roles of design and chance in evolution. This topic is so heated because it touches on fundamental differences between materialistic assumptions and religious faith. However, I argue that molecular discoveries about cellular information processing, epigenetic modifications of the genome, and natural genetic engineering place this issue in a new (?) naturalistic perspective. We can now postulate a role for some kind of purposeful, informed cellular action in evolution without violating any tenets of contemporary science or invoking actors beyond experimental investigation. It remains to be established how "smart" cellular networks can be in guiding genome reformatting and sequence reorganization towards adaptive needs.
Say what?? We have here a 'naturalistic' 'purposeful' action!! On previous occasions I have resorted to using the word 'oxymoronicity'. I think here the phrase 'Oxymoron City' would be more apt. George Orwell could take some pride in this exemplar of Doublethink. Am I being too tough on Jim? That remains to be seen. Perhaps his use of 'new' needs further examination.
James Barham asks important questions on design, teleology and the considers the notion of "thinking matter" ... [more]
[...] No doubt, most readers will assume that empirical science passed a negative judgment on this idea long ago. They will feel that today thinking matter is at best a bare possibility, not a live one. Certainly, the proposition that a certain kind of matter has an intrinsic power of thought flouts the spirit of the Mechanistic Consensus. However, I shall argue below that the Mechanistic Consensus is mistaken in each of its main theses: (1) present-day physics and chemistry do not provide the conceptual resources for a complete understanding of how living things work; (2) natural selection does not provide an adequate ground for naturalizing the normative teleology in living things, which is no mere appearance, but rather objective reality; and (3) thinking is not just a matter of computation, nor does the normative character of thought have anything to do with brains per se. The upshot of these negative arguments will be that living matter is special. Finally, I will conclude on a more positive note by briefly reviewing some ways in which we might begin to understand this specialness scientifically.
Now we're getting down to the nitty-gritty. Is this what Jim S. was talking about? Jim B. continues:
A term like "second messenger," they say, is a metaphor that, while not strictly necessary, is useful in order to avoid intolerably verbose descriptions of the mechanistic interactions that underlie the appearances. Such a façon de parler is a promissory note redeemable in the hard currency of physics and chemistry. But like any IOU, this promise issued by molecular biology is only as sound as the other sciences backing it up. If they cannot make it good, then the note is worthless. Therefore, it behooves us to take a closer look at the conceptual solvency of the Mechanistic Consensus.
[For later reference: BACK TO THE STOICS: Dynamical Monism as the Foundation for a Reformed Naturalism (Talk Delivered at Calvin College, May 25, 2001) JAMES BARHAM. 'Reformed naturalism'? OK, that's what Jim S. must have been alluding to above.] Now continuing from 'thinking matter':
To say that a chemical compound "survives" or that a crystal "reproduces" itself is to employ metaphors that obscure the point at issue. The very thing we are trying to explain is how it is possible for an organism to direct energy in a way that promotes its self-preservation, and not in other energetically equivalent ways. Thus, the notions of survival and reproduction already contain the normative feature of striving to achieve particular preferred states. They are far from the unproblematic mechanistic concepts that a successful reduction would require. Rather, they demarcate the boundary between the living and the nonliving, and so constitute the very heart of the problem of teleology.
Yes, I meant to say that earlier!
However, this does not mean that we are forced to accept the Intelligent Design conclusion. We may just as well reject the premise, instead. In that case, we may say that the "design inference" (Dembski, 1998) constitutes a reductio ad absurdum of the proposition that organisms are machines. If we drop this premise, then we are free to view organisms as active and fully integrated systems, in which a change in one part leads to appropriate changes cascading throughout the system in accordance with functional logic. In this case, evolution begins to make sense from a physical point of view. But now Darwinism has forfeited all of its reductive power! We have simply assumed the functional organization of the cell, which is the very thing we claimed to be able to explain by means of the theory of natural selection.
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