Mod+ 256. DR. DONALD DEGRACIA, WHAT IS SCIENCE?

Sui Huang uses the idea of "intrinsic constraint" by which he means the dynamics of the system. People asked how proteins started folding in the first place. This leads to a regress of questions that can go back to: why does an electron bind a nucleus? The forces, the dynamics, just work out this way. Well, why electrons, why nucleons? That is the standard model of particle physics. Then one asks: why the standard model? That was the point of building the large hadron collidor, to get inside into this issue.

I think that is simplifying a little too much. Nothing for free Don!. In fact the very thing I bring up is the subject of the article linked.

I know there have been studies suggesting what was called "systems controls" directly refering to engineering principles. As in self regulation, James Shapiro has much to say on this. However he cannot explain the emergence of the systems that he determines as driving evolution. It is a perfectly reasonable question to ask. And simply follows the scientific method, discovries lead to new questions. We don't have to regress to the atom. And yet still we should.

http://www.asbmb.org/asbmbtoday/asbmbtoday_article.aspx?id=48961

The article is called "close to a miracle" for good reason.

Overall, what the field of protein evolution needs are some plausible, solid hypotheses to explain how random sequences of amino acids turned into the sophisticated entities that we recognize today as proteins. Until that happens, the phenomenon of the rise of proteins will remain, as Tawfik says, “something like close to a miracle.

If intrinsic constraints is as it's name implies it does not seem appropiate as these are better described as controls and not constraints.
Some protiens can fold and then refold for another function and a billion other dazzling tricks as you know. The range of function is enormous, but the sequences are not. And again as more genomes are sequenced the more singleton proteins are found. I don't see how a constraint will account for the specificity and also the non specificity of some proteins to recognize other proteins as well as misfolds in others, that cut and splice and repair DNA. Ones that can refold for a different function, and even using electrons to test DNA for errors like a circuit. Or so it is assumed.

No one has explained this.

That's a lot of free miracles Don.
 
Yeah, I told you this stuff is a big deal. It is the history that shows how the "soul" got ripped out of science at the very beginning. Here we are 400 years later trying to put it back. It helps to see how it was excised in the first place. Then, people like Searle (or his ilk, not to single him out per se) look more like chumps of this history than anybody we should try to argue with or worry about. It would be great to get The Man himself to come on and discuss this stuff. And of course, I'm happy to talk any time! Glad you took a look at this, Alex. I really do think it is an important part of the puzzle to have incorporated into our thinking.

Best,

Don
yea, I hope we can get Tarpley for an interview, but he's a little cagey... and I'm not sure I agree with where he takes all this. I mean, does this have to be a grand conspiracy spanning 100s of years, or do the consistency applied forces of power/greed/control explain it... or maybe they are one in the same.

Most importantly, I think your work, both in the integration of Yogic thought and in your research applying non-linear dynamics to modern medical problems is key to pulling all this together.
 
Does this make sense?Don

Yeah, it makes good sense. All I will say is that Yoga may not be the only way of providing empirical evidence for oneself. I'm aware of several other traditions that make the same claim, and for all I know, they could all be equally useful. One guy climbs the mountain following one route, and another, another. You find Yoga particularly useful to you, and I find other things useful to me: and I daresay others reading this also have their own particular approaches.

I suppose the most famous allegory is of the blindfolded men feeling an elephant. Un-blindfolded people of course can perceive the whole elephant and the interrelationship of its parts, but how they came to realise they were wearing blindfolds and how they removed them could be very different stories. No matter, the important thing is the seeing of the elephant in its full glory.
 
To skip on the biological jargon, there seems no doubt in the question of proteins, that it is self regulated. This does not tell us much. A protein must have a function. So which came first the protein or the need for the function as well as the systems in the downstream effects? It is somewhat of an engineering feat.

Teleology is easily observed in evolution in the form of convergent evolution. The same systems evolve in different lineages, go extinct then evolve again. It is rampant and very aparent. Darwinists just point to it and say convergent without batting an eyelid. It is a complete contradiction. It exists on the genetic level as well.

However proteins are very diverse, turns out there's a fraction that are specific to each species with no homologues.

IMO it has teleology written all over it. It is a dirty word in biology. But it is there looming over everything.

Yeah. And then there are Hox genes, which govern the development of body patterns in everything from insects to human beings. And curiously, they are very similar although they are involved in the generation of six segmented legs in insects and two arms and two legs in human beings. You can even replace chicken Hox genes with those of a fly without altering normal development.
 
Hi David, thanks for the reply.

Dynamics are just mathematical patterns. Patterns that happen to be of utility for describing material and immaterial systems. When dynamics is applied to thought processes as is currently being done in cognitive psychology, one can rightfully speak of dynamics of an immaterial system.

This is the deep meaning of the word "gunas": they are the dynamical patterns found at all levels of relative being.

That is what I am trying to do with What Is Science? is raise the level of the discourse past all these tired old cliches of materialism, idealism (no offense Michael!), random vs deterministic, etc etc, blah blah blah. These are just encrustations that have gummed up the Western intellect for centuries. Trying to force the yogic ideas in the mold of Western thought is like forcing a college student to read 3rd grade reading lessons. Its an insult to the college student.

Anyway, if you want to trip up a materialist ask them: what is mathematics? Don
I think another of the poorly framed dichotomies is material - vs - immaterial. Immaterial has a connotation of having no substance, hence no structure.

Material vs informational makes perfect sense, instead. Minds process information. Formal information has patterns and has structure, as in logical structure. Further, the semantic information in a message can have patterns and structure. These 3 kinds of structure can all have corresponding patterns. Hence, a chemical pattern, can correspond to complexity in a formal arrangements of bits and the complexity can have semantic meaning for certain receivers.

In a simplified way, a chemical object. like RNA, can correspond to code (as object-oriented programming), which can represent a mental or abstract object. Don, can you comment from your perspective do you observe dynamical patterns at each of these levels of "objects"?

There has been recent philosophical comment that math "objects" could be viewed as a subset of information "objects".

http://link.springer.com/article/10.1007/s12130-010-9096-6#page-1
 
That is what I am trying to do with What Is Science? is raise the level of the discourse past all these tired old cliches of materialism, idealism (no offense Michael!), random vs deterministic, etc etc, blah blah blah.

No offence taken. Matter of fact, I've been trying to say some of this in my recent responses to you. It's just that I'm allowing the possibility that a purely intellectual understanding of Yoga might also be a tired old cliche.

One thing you may not know of is that in the Sufi (and possibly other) traditions, there's the concept of time, place and people. A formulation that might work at one particular time in one particular place for a certain group of people tends to get outmoded and lose its mojo. The underlying truth never changes, of course, but if we try to apply today the whirling dervish dances, say, which Rumi introduced in the 13th century for the rather phlegmatic people of what is now Turkey (because they needed a bit of stirring up), they won't work because the world has moved on and people's psyches are different these days. It's necessary, so the claim goes, that an expert reformulates the system to suit changed circumstances.

But when we look around, we see a lot of fossilisation and loss of dynamism in various erstwhile truly spiritual and effective systems. There's no reason why Yoga couldn't be presented in a form more suitable and effective for modern people, though it would require a skilled teacher to do that, and it might end up being virtually unrecognisable as Yoga. For all I know, such might already exist.

It's also claimed, incidentally, that a time will come when no formulations are necessary: when everyone will be able to realise the Truth for themselves without external guidance. Roll on the day!
 
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have you seen:
wish she woulda followed thru with her Skeptiko interview.

Wow! I have'nt seen this before. I'm wondering why she hasn't posted it at her own blog, which I visit virtually every day. She's one of my heroes: a true scientist and genuine sceptic in the very best sense of that word. Thanks for posting: I'll watch it all the way through later.
 
Hilbert anyone?
220px-Hilbert.jpg


to be brilliant and cool... sometimes a photo says it all.
 
When I use vague terms like 'other people' I'm almost always referring to Alex and his many apologists on this forum.

Another example I would use is Timothy Freke. It's fine for him to talk about many or all of our 'common sense' ideas about the self, freedom and morality being 'illusions', because we know he's a good guy, is 'spiritual', is on our side, etc., but if anybody on the 'dark side' talks about something being an 'illusion' they get absolutely hammered for it, and we're told that their ideas will lead to the end of civilization as we know it.

People here often attack the materialists/atheists/skeptics for the way they seem to delight in undermining our common-sense ideas and showing that everything we thought we knew was wrong, but when other people do this it's OK apparently.

Dominic, you simply don't understand something. Materialists are evil. Materialism is responsible for the continual decline of everything good in the world. Besides, everybody needs to have a respective hate group to... hate. It's good stress relief. It's perfectly fine to treat other human beings like garbage if they don't think like you do (and you've included them in your hate group). This is good for the forum and it's good for Tsakiris. Nobody wants to hear Mr. Mackey interview Craig Weiler-types for months on end. There's gotta be some sandbagging and humiliation every once in a while. Fuck ethics. We're dealing with materialists here. They are everything that is wrong with the world... Lord hear our prayer.
 
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time, place and people. A formulation that might work at one particular time in one particular place for a certain group of people tends to get outmoded and lose its mojo. The underlying truth never changes, of course, but if we try to apply today the whirling dervish dances, say, which Rumi introduced in the 13th century for the rather phlegmatic people of what is now Turkey (because they needed a bit of stirring up), they won't work because the world has moved on and people's psyches are different these days. It's necessary, so the claim goes, that an expert reformulates the system to suit changed circumstances.

wow! this rings true... and connects with some of the ideas about ritual/ceremony we've been kicking around... i.e. maybe ritual is a way to recreate the time, place, people pattern... to create morphic resonance... to tap into the mojo. maybe yoga poses... which BTW sometimes happen spontaneously as a part of STEs... are also a part of this.
 
Wow! I have'nt seen this before. I'm wondering why she hasn't posted it at her own blog, which I visit virtually every day. She's one of my heroes: a true scientist and genuine sceptic in the very best sense of that word. Thanks for posting: I'll watch it all the way through later.
be sure to check out the Q&A at the end, some folks press the issue... her response is interesting.

of course all this plays into what Don is saying about modeling these kinds of systems.
 
Yeah, it makes good sense. All I will say is that Yoga may not be the only way of providing empirical evidence for oneself. I'm aware of several other traditions that make the same claim, and for all I know, they could all be equally useful. One guy climbs the mountain following one route, and another, another. You find Yoga particularly useful to you, and I find other things useful to me: and I daresay others reading this also have their own particular approaches.

I suppose the most famous allegory is of the blindfolded men feeling an elephant. Un-blindfolded people of course can perceive the whole elephant and the interrelationship of its parts, but how they came to realise they were wearing blindfolds and how they removed them could be very different stories. No matter, the important thing is the seeing of the elephant in its full glory.

Hi Michael...just quick...of course yoga is not the only tradition. There are many along these lines, variants of each other. I just happen to know raja yoga the best, and I also find it directly applicable to current scientific ideas like dynamics.

As to the elephant thing:

-Don :)
 

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220px-Hilbert.jpg


to be brilliant and cool... sometimes a photo says it all.
Yeah, I'm obsessed at the moment trying to figure out this guy's deal. I'm reading these essays by Herman Weyl, Hilbert's most successful student. Excuse my French, but that was some crazy shit these guys were involved with at the turn of the 20th century: Cantor, Hilbert, Russel, Godel, Weyl, Turning, Brouwer. What a crazy bunch! These were the guys that ushered in the information age. And they fought like hell about it. Crazy stuff.
 
I think that is simplifying a little too much. Nothing for free Don!. In fact the very thing I bring up is the subject of the article linked.

I know there have been studies suggesting what was called "systems controls" directly refering to engineering principles. As in self regulation, James Shapiro has much to say on this. However he cannot explain the emergence of the systems that he determines as driving evolution. It is a perfectly reasonable question to ask. And simply follows the scientific method, discovries lead to new questions. We don't have to regress to the atom. And yet still we should.

http://www.asbmb.org/asbmbtoday/asbmbtoday_article.aspx?id=48961

The article is called "close to a miracle" for good reason.



If intrinsic constraints is as it's name implies it does not seem appropiate as these are better described as controls and not constraints.
Some protiens can fold and then refold for another function and a billion other dazzling tricks as you know. The range of function is enormous, but the sequences are not. And again as more genomes are sequenced the more singleton proteins are found. I don't see how a constraint will account for the specificity and also the non specificity of some proteins to recognize other proteins as well as misfolds in others, that cut and splice and repair DNA. Ones that can refold for a different function, and even using electrons to test DNA for errors like a circuit. Or so it is assumed.

No one has explained this.

That's a lot of free miracles Don.

I think "nothing for free" applies to relative stuff. Obviously the absolute can do whatever it wants. In this sense you are implicitly agreeing with where I was going in the interview when Alex and I had that brief moment about determinism vs. freedom. Nothing is free in the relative. Not in the energy sense you mean, and not in the normal sense the word "free" is used. Only the absolute is free. It is unbounded in every possible sense. It can even make itself relative and transiently enjoy not being free. Anyway, this line of thought gets to what I said about relative vs absolute being a better way to think than say material vs immaterial, mind vs matter, etc. Western discourse wallows in relative dualisms. There have been periods where relative/absolute was on the intellectual stage, but now is not one of those times in history. Except in math where they use the idea of infinity, which is why I am studying this stuff so closely right now (this is in reference to Alex having posted Hilbert's "duuuude" picture).

Thanks for the article, LS (It's okay to call you "LS", I mean, its not being too informal is it??? :) ). I'm gonna go read it now and will get back to you on it - Best, Don.
 
Hi David, thanks for the reply.

I suggest nuance is in order here. What are dynamics? You can speak of the dynamics of atoms, or the dynamics of stars, or planets, or population biology dynamics, or the dynamics of the heart or brain. .......

I certainly agree that mathematics is non-material - indeed a lot of our reality is non-material Shakespeare's plays, or novels, theories of all sorts etc. All these may use matter to hold a representation of what they are, but they are in essence non-material. However, it seems to me that these represent a passive sort of non-material entity. The dynamics of the solar system doesn't 'decide' to do anything, it is a passive construction that we can use to compute the positions of the planets at a future time. Conceptually it is no different from a huge look-up table.

If you equate your mental self with a mathematical construction, you deny your own free will, and we are back with the old question - why should X (where in this case, X is a piece of mathematics!) experience qualia? I think you need an active non-material entity to experience anything.

I feel we have to get away from the tendency to frame theories like consciousness is X, where X can be anything from an oscillation to a spreading activation, to some sort of computation, to a piece of maths! This approach just goes nowhere, and theories of consciousness of this sort just exist for a while and then go out of fashion to be replaced by another of the same sort!

We may just have to agree to disagree about this - I don't know!

David
 
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The dynamics of the solar system doesn't 'decide' to do anything, it is a passive construction that we can use to compute the positions of the planets at a future time. Conceptually it is no different from a huge look-up table.
Mind if I cut in? Thanks.

You don't know that. And using - what I'd guess from your post is your primary method - intellectual activity ensures a continuation of what you mention - bouncing from one limited concept to another.

It may not deGracia's intent but for me, the point is to develop ways to extend science beyond the intellect
 
In a simplified way, a chemical object. like RNA, can correspond to code (as object-oriented programming), which can represent a mental or abstract object. Don, can you comment from your perspective do you observe dynamical patterns at each of these levels of "objects"?

There has been recent philosophical comment that math "objects" could be viewed as a subset of information "objects".

http://link.springer.com/article/10.1007/s12130-010-9096-6#page-1

Thanks for the link. It is stuff I never saw before but looks like it could be of interest. Too bad for the paywall... As to the levels of "objects" and dynamical patterns, each level is a level of nested dynamical systems. They all are vrittis in the yogic sense, patterns in the mind. As mental patterns they correspond to something in the external world, in a Kantian sense. I don't know if calling each level an "object" is better or worse than calling it a "dynamical pattern". Each view is probably appropriate in different circumstances.

Further, on first impressions, it would seem like the representations could go in many conceivable directions and not just be a strict 1:1 mapping. One man's RNA is another man's food and another man's PhD thesis, for example. Wait....that didn't come out right...hehe. But hopefully you get my point.

Best,

Don
 
No offence taken. Matter of fact, I've been trying to say some of this in my recent responses to you. It's just that I'm allowing the possibility that a purely intellectual understanding of Yoga might also be a tired old cliche.

One thing you may not know of is that in the Sufi (and possibly other) traditions, there's the concept of time, place and people. A formulation that might work at one particular time in one particular place for a certain group of people tends to get outmoded and lose its mojo. The underlying truth never changes, of course, but if we try to apply today the whirling dervish dances, say, which Rumi introduced in the 13th century for the rather phlegmatic people of what is now Turkey (because they needed a bit of stirring up), they won't work because the world has moved on and people's psyches are different these days. It's necessary, so the claim goes, that an expert reformulates the system to suit changed circumstances.

But when we look around, we see a lot of fossilisation and loss of dynamism in various erstwhile truly spiritual and effective systems. There's no reason why Yoga couldn't be presented in a form more suitable and effective for modern people, though it would require a skilled teacher to do that, and it might end up being virtually unrecognisable as Yoga. For all I know, such might already exist.

It's also claimed, incidentally, that a time will come when no formulations are necessary: when everyone will be able to realise the Truth for themselves without external guidance. Roll on the day!
Good points, Michael, one and all. I don't have much to add...
 
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