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The Future of Biology: Reverse Engineering
Creation-Evolution Headlines ^ | 3/14/05 | Staff

Posted on 03/15/2005 2:41:19 PM PST by Michael_Michaelangelo

The Future of Biology: Reverse Engineering    03/14/2005

Just as an engineer can model the feedback controls required in an autopilot system for an aircraft, the biologist can construct models of cellular networks to try to understand how they work.  “The hallmark of a good feedback control design is a resulting closed loop system that is stable and robust to modeling errors and parameter variation in the plant”, [i.e., the system], “and achieves a desired output value quickly without unduly large actuation signals at the plant input,” explain Claire J. Tomlin and Jeffrey D. Axelrod of Stanford in a Commentary in PNAS.1  (Emphasis added in all quotes.)  But are the analytical principles of reverse engineering relevant to biological systems?  Yes, they continue: “Some insightful recent papers advocate a similar modular decomposition of biological systems according to the well defined functional parts used in engineering and, specifically, engineering control theory.
    One example they focus on is the bacterial heat shock response recently modeled by El-Samad et al.2 (see
01/26/2005 entry).  These commentators seem quite amazed at the technology of this biological system:

In a recent issue of PNAS, El-Samad et al. showed that the mechanism used in Escherichia coli to combat heat shock is just what a well trained control engineer would design, given the signals and the functions available.
    Living cells defend themselves from a vast array of environmental insults.  One such environmental stress is exposure to temperatures significantly above the range in which an organism normally lives.  Heat unfolds proteins by introducing thermal energy that is sufficient to overcome the noncovalent molecular interactions that maintain their tertiary structures.  Evidently, this threat has been ubiquitous throughout the evolution [sic] of most life forms.  Organisms respond with a highly conserved response that involves the induced expression of heat shock proteins.  These proteins include molecular chaperones that ordinarily help to fold newly synthesized proteins and in this context help to refold denatured proteins.  They also include proteases [enzymes that disassemble damaged proteins] and, in eukaryotes, a proteolytic multiprotein complex called the proteasome, which serve to degrade denatured proteins that are otherwise harmful or even lethal to the cell.  Sufficient production of chaperones and proteases can rescue the cell from death by repairing or ridding the cell of damaged proteins.
This is no simple trick.  “The challenge to the cell is that the task is gargantuan,” they exclaim.  Thousands of protein parts – up to a quarter of the cell’s protein inventory – must be generated rapidly in times of heat stress.  But like an army with nothing to do, a large heat-shock response force is too expensive to maintain all the time.  Instead, the rescuers are drafted into action when needed by an elaborate system of sensors, feedback and feed-forward loops, and protein networks.
    The interesting thing about this Commentary, however, is not just the bacterial system, amazing as it is.  It’s the way the scientists approached the system to understand it.  “Viewing the heat shock response as a control engineer would,” they continue, El-Samad et al. treated it like a robust system and reverse-engineered it into a mathematical model, then ran simulations to see if it reacted like the biological system.  They found that two feedback loops were finely tuned to each other to provide robustness against single-parameter fluctuations.  By altering the parameters in their model, they could detect influences on the response time and the number of proteins generated.  This approach gave them a handle on what was going on in the cell.
The analysis in El-Samad et al. is important not just because it captures the behavior of the system, but because it decomposes the mechanism into intuitively comprehensible parts.  If the heat shock mechanism can be described and understood in terms of engineering control principles, it will surely be informative to apply these principles to a broad array of cellular regulatory mechanisms and thereby reveal the control architecture under which they operate.
With the flood of data hitting molecular biologists in the post-genomic era, they explain, this reverse-engineering approach is much more promising than identifying the function of each protein part, because:
...the physiologically relevant functions of the majority of proteins encoded in most genomes are either poorly understood or not understood at all.  One can imagine that, by combining these data with measurements of response profiles, it may be possible to deduce the presence of modular control features, such as feedforward or feedback paths, and the kind of control function that the system uses.  It may even be possible to examine the response characteristics of a given system, for example, a rapid and sustained output, as seen here, or an oscillation, and to draw inferences about the conditions under which a mechanism is built to function.  This, in turn, could help in deducing what other signals are participating in the system behavior.
The commentators clearly see this example as a positive step forward toward the ultimate goal, “to predict, from the response characteristics, the overall function of the biological network.”  They hope other biologists will follow the lead of El-Samad et al.  Such reverse engineering may be “the most effective means” of modeling unknown cellular systems, they end: “Certainly, these kinds of analyses promise to raise the bar for understanding biological processes.
1Tomlin and Axelrod, “Understanding biology by reverse engineering the control,” Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0500276102, published online before print March 14, 2005.
2El-Samad, Kurata, Doyle, Gross and Khammash, “Surviving heat shock: Control strategies for robustness and performance,” Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0403510102, published online before print January 24, 2005.
Reader, please understand the significance of this commentary.  Not only did El-Samad et al. demonstrate that the design approach works, but these commentators praised it as the best way to understand biology (notice their title).  That implies all of biology, not just the heat shock response in bacteria, would be better served with the design approach.  This is a powerful affirmation of intelligent design theory from scientists outside the I.D. camp.
    Sure, they referred to evolution a couple of times, but the statements were incidental and worthless.  Reverse engineering needs Darwinism like teenagers need a pack of cigarettes.  Evolutionary theory contributes nothing to this approach; it is just a habit, full of poison and hot air.  Design theory breaks out of the habit and provides a fresh new beginning.  These commentators started their piece with a long paragraph about how engineers design models of aircraft autopilot systems; then they drew clear, unambiguous parallels to biological systems.  If we need to become design engineers to understand biology, then attributing the origin of the systems to chance, undirected processes is foolish.  Darwinistas, your revolution has failed.  Get out of the way, or get with the program.  We don’t need your tall tales and unworkable utopian dreams any more.  The future of biology belongs to the engineers who appreciate good design when they see it.
    It’s amazing to ponder that a cell is programmed to deal with heat shock better than a well-trained civil defense system can deal with a regional heat wave.  How does a cell, without eyes and brains, manage to recruit thousands of highly-specialized workers to help their brethren in need?  (Did you notice some of the rescuers are called chaperones?  Evidently, the same nurses who bring newborn proteins into the world also know how to treat heat stroke.)  And to think this is just one of many such systems working simultaneously in the cell to respond to a host of contingencies is truly staggering.
    Notice also how the commentators described the heat shock response system as “just what a well trained control engineer would design.”  Wonder Who that could be?  Tinkerbell?  Not with her method of designing (see 03/11/2005 commentary).  No matter; leaders in the I.D. movement emphasize that it is not necessary to identify the Designer to detect design.  But they also teach that good science requires following the evidence wherever it leads.


TOPICS: News/Current Events
KEYWORDS: baloney; biology; crevolist; engineering; id; intelligentdesign
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To: r9etb; tortoise; Alamo-Girl; marron; Right Wing Professor; b_sharp; xzins; cornelis; ...
...it seems to me that your example of cherry-picking pi to match specific patterns lends credence to the idea that they're not really separable concepts.

Oh my...what a penetrating insight, r9etb. Thank you, dear man!

551 posted on 03/19/2005 7:56:12 PM PST by betty boop (If everyone is thinking alike, then no one is thinking. -- Gen. George S. Patton)
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To: js1138

"There is no finite description of the phenomena that elicit color perception, and there is no list of wavelengths or combinations of wavelengths that elicit the sensation of color, nor is the same combination of physical phenomena seen as the same by all observers."

There's that word again. "perception"

It has to exist to percieve it. Whether it is the TRUTH is argueable. Color IS, however, and this means that despite tricks our mind may be lead into to think of it, it still IS.

You can take a drug to make you feel happy. This does not mean happines doesn't exist, it means happiness can be counterfeited, which in essence proves it is a universal, as it has a reflective property in our perceptions. Same with colors.


552 posted on 03/19/2005 8:31:29 PM PST by MacDorcha ("You can't reverse engineer something that was not engineered to begin with")
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To: b_sharp

"If it can't be tested, it can not be part of science."

Test "evolution" :p

You can use it to explain things, but that does not mean you can observe it.

Same goes for where our socks go in the laundry. I could explain it by saying "the dryer tore it apart and stuck it in the lent remover" but I can't observe it, so how would it be scientific?


553 posted on 03/19/2005 8:35:18 PM PST by MacDorcha ("You can't reverse engineer something that was not engineered to begin with")
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To: r9etb
I'm not sure that we can really put "knowable" into a nice neat box that is one-to-one with "computable."

I don't think I'm trying to do that. I think that knowable things contain all computable things but not vice versa. I think that all things is the union of knowable things and unknowable things. The unknowable set may be the null set. (Use quotation mrks appropriately.)

554 posted on 03/19/2005 8:42:41 PM PST by AndrewC (All these moments are tossed in lime, like trains in the rear.)
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To: js1138
Picking out a sentence to argue about in the entire context seems to me more-ironic in formula… We all know snowflakes are unique but when we say, “snow” – is it ‘just’ snow and are we rightly left with pi on the face in some frozen circular reasoning. Maybe your ‘wavelength’ is differential and you fixate on color. Although observers might be the only ones seeing it this way…
555 posted on 03/19/2005 8:48:47 PM PST by Heartlander
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To: PatrickHenry; RaceBannon; DannyTN; Michael_Michaelangelo; Alamo-Girl
Speak for yourself, PH.

As usual, there you sit on that larded list-o-broken-links like Jabba the Hut, giving no indication by way of any well-reasoned commentary that you understand a thing that you've linked to, or what relevance it has to any discussion underway. And still, you babble on, acting like you're holding court, as you summon your other ego-inhebriated evo-trolls to their battle stations, to spit their venom and post their own lists-o-broken spam links as they evade their painfully obvious inability to cogently defend their silly positions with objective science.

Too often, your side digresses from a discussion about science into a discussion about religion, because your evo-paganism is threatened to its core by what science actually knows stripped of all the evo-religiosity, counterfeit "scientism", demonstrably false "evidence" peddling (e.g., von Zieten -- just your latest bad-boy example) and all the vain speculation that is fraudulently peddled as fact by your liberal mouthpieces in the MSM. Cowards and intellectual dwarfs -- the lot of you.

Though I have to say, this was a priceless admission for an evo like you from that "Theory of Everything" thread for the other day:

In the past, the great scientific work seemed to simplify the world, and describe it in ways that were relatively easy to understand. If I'm to understand anything more, there needs to be a new simplification, not this 11-dimensional beast that seems to be the most promising bridge between the Einsteinian and the quantum-mechanical world.

It's a bias -- and a hope -- built on my own limitations, but my suspicion is that deep down, and I mean way deep down, the universe is based on a few very simple rules.

Simple rule #1: You evolutionists need to prove you have the time to make happen what is statistically physically impossible to happen.

Simple rule #2: No amount of time exists to make happen what is statistically physically impossible to happen.

Simple rule #3: Without an ability to fulfil simple rule #1, and logically admitting the indisputable fact of rule #2, you must logically conclude that evolution is no "theory" at all, but is at best only a premise and a bias you can merely wish to be true.

Of course, arriving at simple rule #3 requires intellectual honesty in a search for truth in this matter, but too many on your side like Pontius Pilate have looked truth straight in the face and still vainly ask, "What is Truth?" There is none so blind as he who will not see the abundant and screamingly obvious evidence of the intelligent design of the universe which surrounds him.

Now there's the simple truth of the universe in a nutshell.

It's just up to you to summon the courage necessary to get past your own silly ego and smary sophist venom spitters on your team long enough to finally admit to what it is "way deep down" inside that I suspect your 5-senses already know.

556 posted on 03/19/2005 9:13:32 PM PST by Agamemnon
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To: Right Wing Professor
Thank you for your reply! But, er, would you care to elaborate on this sentence (emphasis mine) ...

What surprises me, though, is that people find reassurance in something being unknowable, even though it's exactly determined.

557 posted on 03/19/2005 9:41:12 PM PST by Alamo-Girl
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To: tortoise
Thank you for your reply!

me: it is my hypothesis that algorithm at inception is proof of intelligent design

This is equivalent to saying "existence is proof of intelligent design". Any existence, including a universe filled with nothing but big rocks and no humans. There could not be any existence (and "inception" is really irrelevant) that was not an algorithm. Any state with a Kolmogorov complexity is an algorithm, and I'm sure some would argue that even a state with no Kolmogorov complexity is an algorithm.

I think you missed the point of my hypothesis. It is not the existence of algorithms which prove Intelligent Design - but rather algorithm at inception is proof of Intelligent Design.

When I formulated the hypothesis years ago I used the "Euclid algorithm" (finding the highest common factor between two numbers) as my example. As I'm sure you know, that algorithm includes process, symbol, decision and recursive.

If we see such an algorithm either at the inception of the universe (or multi-verse) or at the inception of life - then it is proof of Intelligent Design. My hypothesis can be falsified by proving that such an algorithm can arise from nothing (universe or multi-verse inception) or from the physical laws/constants (life).

558 posted on 03/19/2005 9:50:13 PM PST by Alamo-Girl
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To: tortoise
Again, thank you for your reply!

me: Nice try, but even one extra temporal dimension violates physical causality.

you:??? That does not follow short of contorting strict definitions with vague semantics. You'll need to explain it.

Not at all. Cumrun Vafa calls it F-Theory.

Some introductory information for anyone interested:

AIP Bulleting 347

SPARE TIME. Descartes gave us co-ordinate geometry, with its three spatial dimensions. Einstein put time on an equivalent footing, creating 4-dimensional spacetime. String theory added six more spatial dimensions, and M theory added yet one more for a total of eleven (see Update 329). Now Cumrun Vafa of Harvard has added still another----an extra element of time---to make the existing theories more compatible with each other. Because of possible side effects, such as faster-than-light travel or questionable causality (time would not be measured sequentially along an axis but would spread out into a plane), Vafa's "F Theory" has not found many adherents yet. (New Scientist, 1 November.)

Two Timing Universe (starting at pg 247)

Evidence for F-Theory

And for anyone who might be thinking Vafa is a light weight, he and Strominger provided the greatest evidence for string theory by using it to arrive at the Hawking-Beckenstein black hole entropy.

559 posted on 03/19/2005 10:05:54 PM PST by Alamo-Girl
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To: tortoise; AndrewC; r9etb
Thank you so much for your post, tortoise! But frankly, AndrewC's reply is superb - exactly in sync with my meaning but much better written. And r9etb's insight was a needed addition to my global statement!

To recap it for any Lurkers:

me: To the contrary, there exist whole domains of subjects which are unknowable - but were they knowable, would be computable.

tortoise: Unknowable in some context does NOT imply non-computable.

AndrewC: Unknowable, does not mean somebody else knows, but I don't. Unknowable, means precisely that, unknowable. It cannot be computed. I might argue that something knowable is not computable. For instance, I know I love my child. Compute it. In any case, if ~Q then ~P is the contrapositive of if P then Q.

I think the logic is...

If x is unknowable then x is not computable. The contrapositive would be If x is computable then x is knowable.

r9etb: I'm not sure that we can really put "knowable" into a nice neat box that is one-to-one with "computable."

AndrewC: I think that knowable things contain all computable things but not vice versa.

To bring this back to Max Tegmark's Level IV multi-verse model - everything in space/time exists as a mathematical structure beyond space/time.

Thus, although everything is a mathematical structure in that cosmology - not everything is knowable, i.e. we can compute what we know - but we may know of something which we cannot compute (adding r9etb's insight here) - and we cannot compute what we do not know.

560 posted on 03/19/2005 10:25:13 PM PST by Alamo-Girl
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To: betty boop
The whole is more than the sum of its parts, taken singly or in any combination.

This is the key!

Life cannot be explained the accumulation of the physical components of any organism. The information (successful communication) in biological systems requires a hierarchical governance - organism, functional molecular machinery, cells.

The fact that the machinery struggles to survive despite a fatal insult elsewhere (e.g. brain death, heart attack) indicates that governance does not necessarily flow top down (or alternatively, that the governance at all tiers is non-local).

561 posted on 03/19/2005 10:51:42 PM PST by Alamo-Girl
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To: betty boop
Thank you so much for your insight and encouragements!

So I will continue to argue that the Universe is more than physico-chemical processes. And the other side will continue to disagree with me. And that's all fine! Let the Lurkers consider both sides of the argument, and draw their own conclusions. Does that sound reasonable?

Sounds great to me! I'll be joining you!

562 posted on 03/19/2005 10:54:10 PM PST by Alamo-Girl
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To: Agamemnon

What a summary!


563 posted on 03/19/2005 11:03:16 PM PST by bondserv (Sincerity with God is the most powerful instigator for change! † [Check out my profile page])
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To: js1138
Thank you for your reply!

You cannot define the color green as a wavelength, or even a blend of wavelengths. You simply can't do it. There is no finite list of properties or phenomena that fully defines the color green.

According to Wikipedia's Physics of Color, green is wavelength interval 550-565 nanometers (vacuum) and frequency interval 600-530 terahertz. They add that "the color table should not be interpreted as a definite list—the pure spectral colors form a continuous spectrum, and how it is divided into distinct colors is a matter of taste and culture".

Getting back to my statement:

The point that you are missing here is that everything in space/time can be expressed as a mathematical structure.

The above is in reference to Max Tegmark's Level IV cosmology. And that statement is unequivocal. It doesn't matter whether one a person knows a thing or not - it is a mathematical structure. One may never be able to compute it because it is unknown, but it nevertheless "is" in space/time and thus is a mathematical structure existing beyond space/time in his cosmology.

564 posted on 03/19/2005 11:06:28 PM PST by Alamo-Girl
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To: betty boop
What an excellent essay post on universals! Thank you oh so very much!!!
565 posted on 03/19/2005 11:07:56 PM PST by Alamo-Girl
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To: Heartlander; betty boop
Thank you so much for your post! There is nothing for me to "hash out". This is great insight:

For any entities x and y, if x and y are really the same thing, then for any property P, P is true of x if and only if P is true for y. If x is the mind and y is a part or state of body (e.g… the brain), then if physicalism is true, x must be identical to y. On the other hand, if something is true of the mind which is not true of some state of the body, then the mind is not identical to the body and physicalism is false. This would even be true if the mind and body are inseparable. The roundness of an apple cannot be separated from its redness. One does not find redness sitting on a table by itself and roundness sitting next to it. But the redness of an apple is not identical to the roundness of an apple. One is a color and one is a shape.


566 posted on 03/19/2005 11:13:29 PM PST by Alamo-Girl
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To: Agamemnon
But how do you really feel? LOLOL! - just kidding.

I see that you are an old-timer on the forum, too - I'm honored by your kudos.

The concerns you have expressed about the decline of morality are shared by many who do not post on these threads. There is considerable resentment that human life has become cheaper - and animal life more precious - since the theory of evolution has been widely accepted.

567 posted on 03/19/2005 11:20:57 PM PST by Alamo-Girl
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To: r9etb; betty boop; StJacques
Thank you so much for your excellent reply!

But if I take what you've said, AG, it seems to me that a universal such as "information (successful communication)" implies purpose, i.e., the intent that the information be perceived, even if it is not.

On that score, perhaps one might be able to differentiate between that kind of "purposeful" information, and the kind of information that comes from our interpretation of the sound we hear when the tree falls in the forest. In this latter case, we (the perceiver) have interpreted an event -- we have supplied information to ourselves, based on an "interrupt." The sound of the falling tree contains no information if there is nothing that can respond to the interrupt.

Indeed, it might be helpful to make that distinction. It seems to me that as soon as some correspondents hear the words "purpose" or "intent" they evidently presume we want to discuss Intelligent Design.

We first began using Shannon's mathematical theory of communications (information theory) in an investigation of abiogenesis. Following that theory there would be a point at which a broadcast would have become autonomous or routed (like in the internet) to individual organisms, molecular machinery or cells.

But as soon as we spoke of a broadcast we were raising the origin of information in space/time (universe). Purpose or intent was not relevant to the investigation and it might have been helpful to clarify that very point.

568 posted on 03/19/2005 11:33:30 PM PST by Alamo-Girl
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To: longshadow; VadeRetro; Junior; All
I'm inspired to add a new section to the List-O-Links, tentatively titled WARNING: THIS IS YOUR BRAIN ON CREATIONISM.
It'll definitely lead off with this: Post 556 by Agamemnon on 20 March 2005.

But that's not enough, so I'm calling for suggestions for a few more classic examples from the past. I realize there are thousands of posts that are good candidates, but I don't want more than 5 or maybe 6 links as a showcase. From time to time, new examples can replace oldies. I'm very enthusiastic about this new group of links.

569 posted on 03/20/2005 4:30:25 AM PST by PatrickHenry (<-- Click on my name. The List-O-Links for evolution threads is at my freeper homepage.)
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To: RightWhale
There is no sound until somebody's ear intercepts the energy and it gets processed in the brain.

That isn't what I am arguing. Light and sound exist whether there are people or not. Pitch exists whether people hear it or not. Wavelengyhs of light exist whether people see it or not.

But color is an interpretation of a sensation. Color does not exist without the eye and brain that create the interpretation. There is no objective definition of color that is complete.

570 posted on 03/20/2005 4:58:14 AM PST by js1138
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To: b_sharp
If the definition is learned while young they will define it the same.

No they won't. People differ in their response to wavelengths of light based on their genetic makeup. There are dozens of genetic variations in color visions.

The simplest way to demonstrate this is with a color matching experiment in which a person tries to match a given color by adjusting an instrument that can produce any blend. People who are not genetically "normal" produce different matches. They cannot learn to produce the "correct" match.

If we had the ability to produce pure monochromatic light of any wavelength at will -- the way an audio oscillator can produce tones of any pitch -- there would be an infinite number of ways to blend wavelengths to produce a color match. Color is an activity of the eye and brain, not an objective phenomenon.

571 posted on 03/20/2005 5:08:03 AM PST by js1138
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To: b_sharp
If we consider how a child learns colour we can see why it is necessarily so.

My first clue that this is wrong came when my son couldn't learn to distinguish red traffic lights from green ones. If the physical equipment isn't there, color isn't there.

572 posted on 03/20/2005 5:11:50 AM PST by js1138
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To: Alamo-Girl
According to Wikipedia's Physics of Color, green is wavelength interval 550-565 nanometers (vacuum) and frequency interval 600-530 terahertz. They add that "the color table should not be interpreted as a definite list—the pure spectral colors form a continuous spectrum, and how it is divided into distinct colors is a matter of taste and culture".

The division of continuous wavelengths into rainbow colors is more a matter of physiology than culture. The labeling may be cultural, but the divisions are based on the fact that we -- most of us -- have three kinds of color receptors. Differences in perception is a result of the fact that people have different numbers of these three types, due to genetic differences. The situation is analogous to the differences people have in tasting bitter things.

573 posted on 03/20/2005 5:24:13 AM PST by js1138
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To: betty boop
The fact that people perceive colors differently for a variety of different reasons does not mean that color is “subjective.” Color must pre-exist before we can even engage in a “dispute” about it. If it didn’t, we couldn’t argue about it.

Your argument in a nutshell:

A class of phenomena exists which we call color. The phenomena exist; therefore, color exists independently of the phenomena.

In 200 posts to this thread, the only objective attempt to define green is via light wavelengths, but this is not a sufficient definition. An adequate definition would at least have to predict whether an objectively defined phenomenon would be perceived as color. Otherwise you are just listing, not defining.

574 posted on 03/20/2005 5:40:26 AM PST by js1138
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To: r9etb
How widely would you cast your net in defining "perceivers" of color? Seems to me that the ability of certain atoms to resonate in response to specific wavelengths of electromagnetic radiation carries along with it all of the basic elements of "color."

You might think so, but this does not explain why humans see bands of color in an equal energy continuous spectrum. The phenomenon of color is created by the eye and brain. The bands of color are an artifact of the way our eyes are constructed, and the fact that most of us have three kinds of receptors. People differ in the ratios of these three receptors and see the bands at different places. People missing one or more kinds of receptor see the bands differently.

575 posted on 03/20/2005 5:48:10 AM PST by js1138
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To: b_sharp
If my wife and I observe a blue-green object we always differ on the amount of green we see in it, not because our perception is necessarily different but because we choose different points along the continuum separating green and blue.

People differ in color matching experiments because they are physiologically different. They have different ratios of the color receptor types. This results in different color matches.

Extreme variations in color receptor ratios are called color blindness, but there are differences more subtle than simply missing one kind of receptor. There are different ratios.

576 posted on 03/20/2005 5:54:31 AM PST by js1138
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To: PatrickHenry
Just point people to DesignedUniverse.com, where the density of good illustrative material is far higher than here. (At least, it was the last time I looked.)
577 posted on 03/20/2005 6:19:31 AM PST by VadeRetro (Liberalism is a cancer on society. Creationism is a cancer on conservatism.)
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To: js1138; r9etb
The phenomenon of color is created by the eye and brain. The bands of color are an artifact of the way our eyes are constructed, and the fact that most of us have three kinds of receptors. People differ in the ratios of these three receptors and see the bands at different places. People missing one or more kinds of receptor see the bands differently.

Are you essentially saying that the universe is fundamentally subjective?

578 posted on 03/20/2005 7:19:19 AM PST by AndrewC (All these moments are tossed in lime, like trains in the rear.)
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To: Alamo-Girl; tortoise
My Internet connection is working at the moment, so I'll attempt one post here. If you're reading this (for any 'you'<>'OhioOAttorney'), then of course it worked.
It is not the existence of algorithms which prove Intelligent Design - but rather algorithm at inception is proof of Intelligent Design. . . . My hypothesis can be falsified by proving that such an algorithm can arise from nothing (universe or multi-verse inception) or from the physical laws/constants (life).

A-G, this is an interesting hypothesis, but I think tortoise's reply still poses a problem for it. If '[t]here could not be any existence . . . that was not an algorithm', then inception really is irrelevant: you will a fortiori find 'algorithm' at the inception of anything you please, because you will always find it anywhere. Perhaps I've misunderstood your hypothesis.

In general, despite my overall agreement with your outlook as expressed in your recent posts, I don't think you're talking about the sort of 'design' relevant to natural selection vs. ID.

As I interpret your posts, you're contending, in effect, that logically intelligible order is evidence of 'intelligence at work'. I don't disagree, but this point applies pretty much across the board to rocks, horses, and aircraft -- indeed to anything that exists (I know you and I agree that the universe is logical in at least the minimal sense of 'logically consistent').

A similar objection seems to apply to your invoking of universals; even if we agree about them otherwise, 'blind' physical laws rely on them just as surely as algorithmic natural selection does. (By the way, there have been philosophers who have accepted the existence of real universals and remained generally committed to scientific naturalism, two recent examples being Brand Blanshard and David Malet Armstrong. They don't have much else in common -- for example, Armstrong is pretty confident that mind reduces to matter and Blanshard was utterly convinced that it does not -- but both of them are/were 'naturalists' in the sense that they don't/didn't think 'natural vs. supernatural' tracks any genuine distinction in objective reality. Incidentally, the reason for the awkward changes of tense in the last couple of sentences is that Blanshard is dead and Armstrong is not.)

What's at issue in ID is whether something was 'designed' by an intelligence looking ahead in time (from within some appropriate frame of reference) and in effect saying, at time t0, 'Let there be [such-and-such] at time t1' where t1>t0. I don't think ID argues plausibly for this sort of 'design', and (as I suggested briefly in an earlier post, I'm not sure this makes any sense as applied to a timeless/eternal God either.

As far as I can tell, nothing about the theory of evolution by natural selection at the genetic level affects these issues one whit. If the theory is true&nbdp;-- as I think it is&nbnsp;-- it leaves all that nifty stuff about universals and intelligible order and God and so forth right where it was.

I've lost track of who all might want to be pinged on this, so please don't take it personally if I've excluded you. A-G, if there's anyone you think would be interested, please feel free to ping them on any reply you may post. (And if I don't get back to you soon, it probably just means my connection is on the fritz again.)

579 posted on 03/20/2005 7:44:03 AM PST by OhioAttorney
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To: OhioAttorney
HTML typos where nonbreaking spaces should have been: 'If the theory is true -- as I think it is -- it leaves all that nifty stuff about universals and intelligible order and God and so forth right where it was.'
580 posted on 03/20/2005 7:46:32 AM PST by OhioAttorney
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To: Agamemnon
In RWP, you are debating an outed existentialist.

You mean, like Sartre?

You obviously haven't got a clue what an existentialist actually is.

RWP is the center of gravity within his vanishingly small universe, which itself resides within the mere 3.5 lbs of grey matter sitting atop a frame desperately in need of student worship.

On the other hand, in Agamemnon, we have an idiot savant whose verbosity vastly exceeds his erudition.

We've been through the phony attempts to blame Hitler (a Christian, who claimed he was doing God's work) and Stalin (who persecuted Darwinists) so often, I have no intention of rehashing them. Tendentious, tiresome, and fundamentally dishonest.

581 posted on 03/20/2005 8:03:40 AM PST by Right Wing Professor
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To: AndrewC
I think that knowable things contain all computable things but not vice versa.

This is what I meant by "it needs to be qualified". Knowable in what context? The only way your above statement could be true is if the observer ("knower") is a true universal Turing machine. Unfortunately, UTMs (or the functional analogs, for the sake of discussion here) do not exist in this universe. If you are stuck with nothing but plain old finite Turing machines for observers, like humans, your statement is false.

I'm trying to figure out a context in which your statement both makes sense and has utility in this discussion.

582 posted on 03/20/2005 8:40:42 AM PST by tortoise (All these moments lost in time, like tears in the rain.)
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To: js1138
Thank you for your reply!

The division of continuous wavelengths into rainbow colors is more a matter of physiology than culture. The labeling may be cultural, but the divisions are based on the fact that we -- most of us -- have three kinds of color receptors. Differences in perception is a result of the fact that people have different numbers of these three types, due to genetic differences. The situation is analogous to the differences people have in tasting bitter things.

It seems to me that you do not dispute the spectrum of color nor that each color has been assigned an objective wavelength interval and frequency interval - but rather that the color can only be understood subjectively, as a perception of an individual. In which case, IMHO, it is semantics, so again I assert:

The frequency (color) must exist before it is perceived (color) and therefore color (frequency) is a universal whereas color (perception) is not.

583 posted on 03/20/2005 8:49:57 AM PST by Alamo-Girl
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To: PatrickHenry; RaceBannon; DannyTN; Michael_Michaelangelo; Alamo-Girl; Agamemnon

It is my undertanding, that though insultingly throwing out another post at Agamemnon... Nothing has been addressed aside from Elistism on the side of the evos.

PH- Dispute, don't insult.


584 posted on 03/20/2005 8:55:21 AM PST by MacDorcha ("You can't reverse engineer something that was not engineered to begin with")
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To: Alamo-Girl
The frequency (color) must exist before it is perceived (color) and therefore color (frequency) is a universal whereas color (perception) is not.

You sure 'bout that? Your argument seems to me to show that they're not the same universal (since apparently one has a property the other lacks), but it doesn't show that 'color (perception)' is not a universal at all.

Forget color names, forget light frequencies. Right now, in one small region of my visual field, I'm experiencing a particular quality of the kind 'color (perception)'. That specific quality -- no matter what name we give it, and no matter what underlying physical cause we assign to its occurrence in my visual field -- that quality can occur repeatably, and its other occurrences seem to be (qualitatively) identical to it. So isn't that quality a 'universal' quite independently of whether it exists prior to perception? (And, of course, independently of whether we can give an objective 'definition' of it?)

585 posted on 03/20/2005 8:59:04 AM PST by OhioAttorney
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To: Alamo-Girl
If we see such an algorithm either at the inception of the universe (or multi-verse) or at the inception of life - then it is proof of Intelligent Design.

Except that there will always be an algorithm at inception, and there is a high probability of Turing completeness with whatever algorithm actually exists at inception. We get that for free without having to invoke Intelligent Design. There are scads of very tiny TC calculi that require almost no information to exist, and which are very likely to exist in any vaguely complex system.

Even if we have such an algorithm at inception, it lends little support to the notion of Intelligent Design since there is a good probability that a random sampling of the initial algorithm phase space will give you the same result. If TC algorithms were very rare it might make a more interesting argument for Intelligent Design, but that seems unnecessary on its face since one cannot even make an argument of statistical improbability here. Occam's Razor. I'd lay your hypothesis to rest on this basis alone.

And of course, the good old anthropic principle still applies to your basic argument, regardless of the probability of Turing completeness.

586 posted on 03/20/2005 9:06:27 AM PST by tortoise (All these moments lost in time, like tears in the rain.)
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To: js1138

I get what you have been saying as far as "machines" and colorblind people wouldn't percieve certain tricks as "color" and therefore "color" should not be a universal. Because it can be percieved without actually being said color.

HOWEVER (and if that didn't make sense, I'll elaborate on it later per request) if one can trick an eye into seeing what something isn't, this simply means you can mimic color, it does not change the wavelength of the true color.

Showing me a disc that when spun looks "green" does not mean "green" isn't universal, it means the disc can look it.

It's like saying "oh look, a Stick Bug! I guess that means sticks are subjective."

No it means sticks can be falsified by other things.

In addition, grear arguements so far. No wonder our philosphers of years past were so stumped. We've got the Internet and it's still hard to arrive at a consensus.


587 posted on 03/20/2005 9:07:08 AM PST by MacDorcha ("You can't reverse engineer something that was not engineered to begin with")
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To: MacDorcha

*Elistism=Elitism.... or is the Lysdexia?


588 posted on 03/20/2005 9:08:56 AM PST by MacDorcha ("You can't reverse engineer something that was not engineered to begin with")
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To: MacDorcha

Elite Placemarker


589 posted on 03/20/2005 9:11:32 AM PST by Michael_Michaelangelo (The best theory is not ipso facto a good theory. Lots of links on my homepage...)
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To: Alamo-Girl
Elaborating...

Your claim is that a second time dimension precludes causality. I'm willing to grant that (it at least seems plausible). But nonetheless, the evolution of the universe (using evolution in the mathematical and not biological sense) is as deterministic with a second time dimension. We still have a massive set of coupled differential equations which have a definite solution, albeit an uncomputable one. What we are and what we do depends on the state of us and the universe, and on nothing else. That's determinism (or maybe predestination, if you prefer the term).

Now all of the pseudo-moral objections to determinism apply with equal force to this model; we are, after all, only a further operation of a set of conditions and laws. The fact we can't feasibly (and maybe can't at all) predict the result appears to me not to bear at all on the matter.

Now I happen to believe that the fact that we are subject to physical laws and external conditions does not absolve us from full responsibility for our actions, so I don't have a problem with this. I'm not sure of your position on the issue.

590 posted on 03/20/2005 9:12:26 AM PST by Right Wing Professor
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To: Right Wing Professor

We've been through the phony attempts to blame Hitler (a Christian, who claimed he was doing God's work) and Stalin (who persecuted Darwinists) so often, I have no intention of rehashing them. Tendentious, tiresome, and fundamentally dishonest.

Lets just get it all straight here and now:

Hitler was (claimed to be) a Christian, who followed Darwin to excuse what he did.

Stalin was an atheist, who killedDarwinists AND Christians because they both supported that Man was indeed something special. They both also represented "thought" and "free-will" in the mere fact that they had the capacity to think on those levels.

Both are good examples of knowledge in the hands of evil people.


591 posted on 03/20/2005 9:15:41 AM PST by MacDorcha ("You can't reverse engineer something that was not engineered to begin with")
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To: MacDorcha; js1138
Showing me a disc that when spun looks "green" does not mean "green" isn't universal, it means the disc can look it.

Agreed. I think you and I are saying pretty much the same thing on this point (see my post #585).

In addition, great arguments so far.

We're agreed on that too. I was just thinking a few minutes ago that there's been a very impressive level of argumentation on this thread.

592 posted on 03/20/2005 9:16:14 AM PST by OhioAttorney
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To: Alamo-Girl
Cumrun Vafa calls it F-Theory.

My objection is primarily to the notion that this changes the basic nature of the computational fabric of the universe, something which does not really follow. Most of the consequences are to a conventional pedestrian perspective of such things, from a fundamental math perspective it doesn't really change anything i.e. everything previously stated from that layer of theory still holds even if the physical model is changed to this one. Since I'm working at the more fundamental math layer, I'm missing the importance of this theory to the mathematical arguments.

593 posted on 03/20/2005 9:16:59 AM PST by tortoise (All these moments lost in time, like tears in the rain.)
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To: OhioAttorney; tortoise
Thank you so much for your reply! It is always a delight to read your analyses.

A-G, this is an interesting hypothesis, but I think tortoise's reply still poses a problem for it. If '[t]here could not be any existence . . . that was not an algorithm', then inception really is irrelevant: you will a fortiori find 'algorithm' at the inception of anything you please, because you will always find it anywhere. Perhaps I've misunderstood your hypothesis.

Indeed, I’m failing to get the point across here.

“At” inception does not mean a property of the thing emerging but what is required for it to emerge. That all existents are algorithmic is utterly beside the point of my hypothesis.

In a nutshell, my hypothesis says that if an algorithm is required to give rise to a thing, then it is proof that the thing is intelligently designed.

The algorithm I have in mind is not a least description formula, such as Kolmogorov complexity, but rather a Euclid algorithm which includes process, symbol, decision and recursive. These are elements of intelligence per se.

The “inception” I had in mind was the universe (big bang or multiverse) or life (abiogenesis v biogenesis) – but the same hypothesis could be applied to any “thing”. IOW, if an algorithm was required to give rise to a thing, then it was intelligently designed.

Since it speaks only to inception – and the theory of evolution does not speak at all to origins or “what is life v non-life/death in nature” – my hypothesis has no direct relevance to the theory of evolution. It is however directly relevant to intelligent design.

As I interpret your posts, you're contending, in effect, that logically intelligible order is evidence of 'intelligence at work'. I don't disagree, but this point applies pretty much across the board to rocks, horses, and aircraft -- indeed to anything that exists (I know you and I agree that the universe is logical in at least the minimal sense of 'logically consistent').

I do agree with your point here, but it was not the scope of my hypothesis about inceptions.

What's at issue in ID is whether something was 'designed' by an intelligence looking ahead in time (from within some appropriate frame of reference) and in effect saying, at time t0, 'Let there be [such-and-such] at time t1' where t1>t0. I don't think ID argues plausibly for this sort of 'design', and (as I suggested briefly in an earlier post, I'm not sure this makes any sense as applied to a timeless/eternal God either.

I’m not aware of anyone suggesting that a designer was looking ahead from within space/time. That would not be a wholly off-the-wall speculation though, were the designer (a space alien for instance) mentally and visually capable of perception from more than one time dimension.

IOW, most predestination musings on the subject would involve a designer who is “beyond” space/time altogether. Usually this would be seen as God but some might say the designer is “a universal collective consciousness”.

The fact that all cosmologies require a beginning (geometry or space/time from the big bang or pre-big bang geometry or space/time) points to the existence of an “uncaused cause”. God is the only candidate for uncaused cause. As such, since there is nothing of which anything could be made but Himself (or more specifically, His will) – He not only is “beyond” space/time and everything else that comprises “all that there is” but transcends it as well.

Of course theologians argue endlessly on the properties of God – but the point of agreement IMHO would be that He is unknowable in His fullness.

594 posted on 03/20/2005 9:21:54 AM PST by Alamo-Girl
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To: OhioAttorney
Thank you so much for your reply!

Forget color names, forget light frequencies. Right now, in one small region of my visual field, I'm experiencing a particular quality of the kind 'color (perception)'. That specific quality -- no matter what name we give it, and no matter what underlying physical cause we assign to its occurrence in my visual field -- that quality can occur repeatably, and its other occurrences seem to be (qualitatively) identical to it. So isn't that quality a 'universal' quite independently of whether it exists prior to perception? (And, of course, independently of whether we can give an objective 'definition' of it?)

Indeed, this is looking at "color" as also being qualia and that qualia are universal!

Another example would be pain - which is experienced personally and cannot be communicated to anyone else. I would say "pain" is a universal also.

But that is taking off my "let's find common ground" hat trying to separate the physical and measurable universals from the qualia - and putting on my subjective (radical mathematical Platonist) hat whereby I agree with Max Tegmark's Level IV cosmology. IOW, they are not only universals but are also mathematical structures which actually exist "beyond" space/time.

595 posted on 03/20/2005 9:29:57 AM PST by Alamo-Girl
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To: tortoise; OhioAttorney
Thank you for your reply! But, er, I just posted to OhioAttorney and pinged you in an attempt to clarify what I meant by "at" inception. Please let me know if your objection is the same after that post.

And of course, the good old anthropic principle still applies to your basic argument, regardless of the probability of Turing completeness.

I reject the anthropic principle argument as the equivalent of saying "God did it!" because it essentially means "Nature did it!". Both shut down further investigation needlessly.

596 posted on 03/20/2005 9:34:13 AM PST by Alamo-Girl
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To: AndrewC
Are you essentially saying that the universe is fundamentally subjective?

I'm not arguing that. I'm arguing that there are perceptions that are artifacts of our physiology. Pi and the number three are not particularly tied to our physiology, but color is. Color is not entirely different from commonly known optical illusions. The bands of color in the rainbow do not have an objective existence. The energy of sunlight is evenly distributed across all visible wavelengths. We see bands because our eyes have receptors that have nonuniform responses to different wavelengths, and because the neurons associated with vision encode the differential output of the receptors.

This might be considered objective, except for the fact that the encoding of color can be spoofed by other phenomena, such as the flickering of a monochromatic light source, which can induce the perception of colors other than the source.

If you could catalog all the phenomena that produce the perception of color, you might be able to argue that color has an objective existence, but you can't. At best you can produce specific engineering solutions for producing color monitors and color printers. But even these are not perfect. Different populations of humans have slightly different responses to color and match colors differently. This is not just culture. Culture naming and color preference might be cultural, but color matching experiments show that people can see color differently.

597 posted on 03/20/2005 9:36:06 AM PST by js1138
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To: Alamo-Girl
“At” inception does not mean a property of the thing emerging but what is required for it to emerge. . . In a nutshell, my hypothesis says that if an algorithm is required to give rise to a thing, then it is proof that the thing is intelligently designed.

Oh, okay; thanks for the clarification.

Doesn't this argument show, if anything, that if an algorithm is necessary to produce X, then the algorithm is intelligently designed? How does it show anything about X itself? In other words, how does it distinguish between a God who 'makes X via the algorithm' (which would be odd anyway, as an omnipotent God would presumably just 'make X' directly) and a God who 'makes the algorithm of which X happens to be a fortuitous byproduct, not itself designed'?

I’m not aware of anyone suggesting that a designer was looking ahead from within space/time.

Well, the IDers say their arguments say nothing at all about what sort of designer is doing the designing. But since they distinguish (as your arguments apparently don't) between rocks and aircraft, I think they must be talking about the sort of design that involves conception temporally prior to the existence of the object, whether they intend to do so or not.

At any rate, as far as your own arguments are concerned, I think they apply to rocks (and the results of 'blind' physical processes generally), so even if they're true they don't seem to get at ID as the IDers understand it. If you're right, then you've successfully shown that rocks are the product of intelligence as well, and this is precisely what the IDers claim not to be able to show; that's why, whenever they find something 'rocklike' in this respect, they drop it and keep looking for something 'airplanelike'.

[T]here is nothing of which anything could be made but Himself (or more specifically, His will)[.]

That's essentially my own view as well.

598 posted on 03/20/2005 9:38:07 AM PST by OhioAttorney
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To: Alamo-Girl
my hypothesis says that if an algorithm is required to give rise to a thing, then it is proof that the thing is intelligently designed.

This is more a tautology than a hypothesis. "If an algorithm is required to give rise to a thing"? Why "if"? That is always true.

Also, it has been established in the past many, many times that it is mathematically impossible to prove design. Building a hypothesis that nominally "proves" something that is provably impossible is not useful. It is a giant step backward if these long dead horses are being resurrected for another round of flogging. A feature of these discussions is that canards get reinserted as facts down the road after they've already been soundly put to bed, only to get hammered down again.

The algorithm I have in mind is not a least description formula, such as Kolmogorov complexity, but rather a Euclid algorithm which includes process, symbol, decision and recursive.

Six of one, half dozen of the other. Every Euclid algorithm has a Kolmogorov complexity and can be losslessly reduced to basic algorithmic information. This is not a mathematical escape hatch.

599 posted on 03/20/2005 9:39:51 AM PST by tortoise (All these moments lost in time, like tears in the rain.)
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To: Alamo-Girl
But that is taking off my "let's find common ground" hat trying to separate the physical and measurable universals from the qualia - and putting on my subjective (radical mathematical Platonist) hat whereby I agree with Max Tegmark's Level IV cosmology. IOW, they are not only universals but are also mathematical structures which actually exist "beyond" space/time.

And in this sense, of course, even those subjective, perceptual qualia, as impossible as it is for them to exist apart from at least the possibility of experience, do nevertheless exist timelessly in at least three distinguishable ways: as qualities, as causal potentialities, and as logical possibilities. This radical mathematical Platonist agrees with you on that, while also agreeing that the rest of the discussion in this thread doesn't require such agreement.

600 posted on 03/20/2005 9:48:40 AM PST by OhioAttorney
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