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

exon shuffling and alternative splicing are far from simple processes! The fact that one gene sequence can apparently produce many different gene products to my mind speaks of a lot of implicit organisation and greater economy of resource utilisation.

Yes, nothing for free. A bit like co option theory. If you keep borrowing parts from other systems, eventually you are left with borrowing from nothing.
Does another layer of control make things any easier? Systems control, much like the immunology model hey Michael? Except there does not seem to be a trial and error process. At the protein level that could be disastrous.

The cell writes new proteins by splicing and rearanging, more than that some cells can completely rearange thier DNA. Certainly not Darwinian by any stretch of the imagination.
 
Hi LoneShaman

As dynamical patterns, gunas indeed represent something. They are "signs" of the intent of the consciousness at their base. Just as we - our physical bodies and minds - are expressions or representations of the consciousness at our base. This is the grand insight of yoga I try to emphasize in What Is Science? I link it back to a panpsychic point of view, which it is, but also is not. Panpsychism is an idea or philosophical position. The yogic ideas claim to be empirical. I cannot justify this other than what was said in the interview. I have had elementary experiences of this nature and infer the more advanced experiences will work as advertised.

Yes, this is what I first recognized from your posts reflected in my own views. That certainly resonates with me.

When you ask: where does meaning come from? My answer is: this is one reason I have come to accept the yogic framework. It at least offers a plausible answer. It is the base of all things, everything comes from it. Consciousness is the source of meaning. But we must flip everything upside down. Reductionism gets inverted. The irreducible thing is consciousness, being, and from this all things are formed. On this basis it is clear that no material interaction per se can generate meaning. They are the effect, not the cause of meaning. But meaning is not the base, consciousness is. But consciousness cannot be formalized in any sense and so meaning must be the plaform on which this whole edifice is.

Same bottom line. And I have a better idea of where you are coming from.

Thanks for your reply Don. Very interesting. Hopefully I can add some more, but I would need more familiarty with the concepts.
 
Hi LoneShaman

We'll now we are getting somewhere with the dynamics stuff! Now, I don't think it is so much an agree/disagree thing. Instead, let's try to seek clarification. I have suggest dynamics of non-equilibrium systems will be the core method for modeling life, and all structures that exist. I suggested other methods will go by the wayside and mentioned "information" as one of these methods. Ok, so you counter that information underlies the dynamical patterns. Great. Let's get deeper into this.

I'd like to clarify something here. I mean on the face of it, the dynamics of non-equilibrium systems is a totally materialistic concept - which wouldn't really offer scope for the involvement of the non-material in any way.

However, systems close to chaos could obviously be controlled if an entity had a way to select a few critical quantum transitions - providing it was somehow possible for that entity to know what to do. Chaos magnifies tiny changes into macroscopic ones. One way it might know would be if it could see the consequences of multiple quantum choices for some distance into the future.

I have speculated that this is related to Dean Radin's presentiment. Does our non-physical self pick quantum eigenfunctions on the basis of knowledge of multiple possible futures?

I hope the above makes sense!

David
 
I'm asking the question naively, not as a challenge, because I'm not very familiar with yogic thought - but reading this thread, the question that I keep having is: what is the argument for those yogic revelations being ontologically superior or more basic to other types of altered state experiences? Other than to the person experiencing that non-duality in a deep meditative state, what makes that experience more basic than a deep NDE, say? Is the argument based on the fact that it's philosophically more convincing to some, or that they personally resonate with it more?

I'm a little late to this party so this may have already been hashed out, but I think the systematic one-pointedness of the Yogic thought is the initial appeal. then Don's saying that since his personal experiences lined-up with the sutras re the basics, he was inclined to believe they may be accurate for the unexplored territory.
 
Materialists have their own metaphorical solutions to the Hard Problem - if we're going to hold their feet to the fire for a real answer the same should, IMO, be expected of anyone offering a philosophical/scientific solution the question of how One becomes Many while still really being One.

one minor quibble... it seems to me that materialists/scientists/atheists make a more fundamental/categorical error. more like the "not even wrong" thing. I don't think the comparison is fair.
 
Thx for this interesting link. As I was reading I couldn't stop thinking of you're previous reference to the Spy Vs. Spy comics :)

I can't find it in me to feel much sympathy for the fallen guru. as far as the grander spiritual meaning, mundane explanations of power, greed and sex fit well enough.

One that I can't quit process is Maharishi Mahesh Yogi... I get his misdeeds, but how can all those folks at Maharishi University go on pretending none of this stuff happened. I mean, this is recent history. Modern-day cult-making in action.
 
Hi David

The easiest example off the topic of my head are the steroid receptors, say the estrogen or progesterone receptor. You may or may not know that these proteins float inactive in the cytoplasm and when they bind the steroid, they transport to the nucleus and act as transcription factors, binding to specific DNA sequences and causing increased transcription of the hormone-sensitive genes.

So, the separable domain functions are:

1. Bind the steroid
2. Bind a specific DNA sequence
3. Activate DNA transcription.

You can "mix and match" these proteins. You can take the estrogen binding domain of the estrogen receptor and swap it out for the progesterone binding domain of the progesterone receptor. Then, when you give estrogen, it activates progesterone-responsive genes.

You can replace the DNA binding domain of the estrogen receptor with the progesterone receptor's DNA binding domain. Then, when you give estrogen, it activates progesterone -responsive genes.

This is old stuff nowadays. There are many other examples. I could go into some from my own area of ribosome regulation, but it would get incomprehensible fast probably.

Another way to see this. Maybe you have heard that genes are stored in the DNA as introns and exons. Introns get cut out and discarded when the DNA is converted to mRNA in the nucleus. Then, the exons are pasted together to make the mature mRNA. It turns out that in the vast majority of cases, the exons are coding the distinct protein domains.

So, no, it's not something that merits skepticism. There is overwhelming evidence that this is how the DNA and proteins are organized at this point. I don't know how alcohol dehydrogenase functions. I could look it up and tell you, but am too lazy right now...sorry! :)

Don

Maybe you are somewhat making my point. The module approach only reduces the 'design' cost for enzymes which perform a series of stages. A lot of enzymes - e.g. presumably the ones that power the Krebs cycle only perform one step or maybe two at most. I still feel those ID proponents that point out the overwhelming combinatorial cost of exploring 'protein sequence space' have a strong point.

David
 
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Thx for this interesting link. As I was reading I couldn't stop thinking of you're previous reference to the Spy Vs. Spy comics :)

I can't find it in me to feel much sympathy for the fallen guru. as far as the grander spiritual meaning, mundane explanations of power, greed and sex fit well enough.

One that I can't quit process is Maharishi Mahesh Yogi... I get his misdeeds, but how can all those folks at Maharishi University go on pretending none of this stuff happened. I mean, this is recent history. Modern-day cult-making in action.

The Maharishi, Osho, Andrew Cohen...there's a bunch of them. There is a tradition of malamati in Sufism where teachers will deliberately court opprobrium by giving the appearance of impropriety (to discourage dilettante followers), but I don't know if it's ever applied in other traditions. Whatever, they can't all be malamati. Osho is the one who puzzles me most because some of his writings are quite sublime.

There's something else that Idries Shah mentioned: the phenomenon of earth sickness as he called it, to which everyone, including high spiritual attainers, may succumb. If you work in a coal mine, though you be a saint, you'll get black just like anyone else...
 
Here's an analogy
.

I am cryptic as has been pointed out. Do you get it?

The materialist will say it is just sand under the influence of kinetic energy and gravity.
Beautiful isn't it? Brings people to tears in the audience, and it isn't the sand. It's the symbols, the emotion and the patterns of sound waves that tell the story.
 
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Regarding exon shuffling, this is also relevant...

The fact that mutation might not be random doesn't help explain the production of biological information. Conservation of information requires that non-random searchers have built in information that is greater than or equal to the information produced by a random search. If non random mutation makes beneficial mutations more likely, then the information needed for a system that involves non-random mutations to arise, requires information greater or equal to the new biological information it produces.

Similarly the no-free-lunch theorem shows that any search of the fitness landscape will be no better than chance unless there is information built into the search.

http://www.evolutionnews.org/2012/08/conservation_of063671.html


http://www.evoinfo.org/papers/ConsInfo_NoN.pdf
 
I am cryptic as has been pointed out. Do you get it?

The materialist will say it is just sand under the influence of kinetic energy and gravity. Beautiful isn't it? Brings people to tears in the audience, and it isn't the sand. It's the symbols, the emotion and the patterns of sound waves that tell the story.

Bravo, LS! There are the messages in the sand images, and then above and beyond that, the message you've used it to convey, which in the end is inexpressible in words: a felt experience rather than an intellectual understanding. It is this experience that materialists may also feel on occasion, but if so, they suppress and obfuscate it for themselves. I think it's actually very sad for them.

Maybe you could have been even more concise and shortened your text to: "Sand under the influence of kinetic energy and gravity". Ceci n'est pas une pipe and all that. But then, some might have thought you too cryptic:

MagrittePipe.jpg


Your poem is quite the most memorable I've come across on this forum. I think I'll take it with me to my grave.
 
OK, this and your previous post help quite a lot. I find it interesting also that exons, separated by introns, can map to specific protein domains: that opens up the theoretical possibility that the same exon in the same location could be used in the formation of different proteins--does that happen, I wonder? It would make for a highly modular system. Or, rather, can the same exon be found repeated in different gene sequences? I guess the latter is asking if a specific intron/exon sequence is unique to the production of a specific protein, even though the same exon might be found in different gene sequences.

I must say that I lean towards Loneshaman's view that Shannon information isn't semantic, which you also seem to agree with. There is meaning at the bottom of everything, of that I'm convinced, and meaning can only arise in consciousness, which latter is what it is and has no progenitor. One can think in terms of Panpsychism or Idealism (which is my own personal preference), or whatever: I don't suppose any of us know for sure. I'm getting the feeling that a lot of us are coming to similar conclusions, and only really differing in our preferred interpretations of what's going on. In that sense, it may not be so important whether one leans towards Yogic explanations, or something else. The main issue with that is that different interpretative systems use different concepts and terminology: but I suppose they could in the end be largely isomorphic.

Everyone knows that Shannon information is not semantic. It is a formal model of coding. The fact that it lacks the ability to model meaning is both a limit and a strength of the model. You can see this in how computers work: a digital image, audio file, or word processor document all reduce to the same thing, a string of 1s and 0s. To us, they all mean something different, to a computer they are all the same. Computers and the internet would not be what they are without this sterile view of information.

The bold thing I am saying in What Is Science? about yoga is that it is not an explanation, not in the sense of any philosophical explanation. It is a set of methods and practices that, if one learns to do successfully, it will allow one to experience the answer to these questions. Now, we can talk about what yogis describe and turn it into a philosophical position, but this defeats the purpose and just puts us back where we started from, which was not my intent. It's like intellecualizing NDEs. Just go learn to OBE for yourself and have the experience. NDEs are another way to get there, not one I would personally advocate, but it takes you to the same "place".

The best metaphor I have for my viewpoint at the moment is this. Imagine it is 1690 and you are in a pub in England. In walks this guy, Robert Boyle. Now, you have to imagine the world in 1690. There is no science as we know it. Newton's stuff is one generation old, and is esoteric stuff known by few. No electricity, etc. And you and some friends are sitting in the pub debating the alchemists vs the atomists of Democritus. In walks Boyle and says, hey, I can convert wood to a few different types of atoms, or I can convert rock to some other different types of atoms. At that time, Democritus' idea of atom meant that everything was made of the same atom. There was only one type of atom and everything was made of it. And you and your friends are sitting there speculating on what this ultimate atom of matter was,what its nature was.

And Boyle joins the conversation and starts adding all these weird new ideas. And you and your group think he is just another philosopher. But he says, no, this is not philosophy...come with me. And he takes you back to his estate and in his barn is one of the first chemistry labs the world has ever seen. And he shows you how to convert a rock or piece of wood to its constituent atoms. What Boyle was doing was not philosophy, it was something else, something we eventually came to call "chemistry" and was a branch of what eventually became "science".

This is how I look at yoga. It is like walking into Boyle's lab when there were no other labs in the world. Yoga is a set of methods for achieving altered states. And you learn things in these altered states. That is what I am saying in What is Science? and even is the question Alex asked about at the top of the thread.

The Boyle metaphor, though seemingly oblique is the best I have at the moment. If you have never read the Skeptical Chymist, you should check it out. The wiki page has links to the book itself. It transports you to a time when there was no chemistry as we understand it. Boyle was the first to understand modern chemistry, not through philosophy but through actually doing it.

So, while I am forced to sit here and express these ideas and they sound like philosophy, the most important thing I can do is help you learn the methods. Like in DO-OBE, or in WIS where I outline the methods of yoga enough to get someone started on them.

Does this make sense?

Thanks, Michael!

Best,

Don
 
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.
 
Thankyou most kindly Don for your personal reply. I will listen to the podcast again and have a look at your other work. Sorry if I took some of your statements out of context, a lot of it is probably above me. Perhaps I should have said that I found the show hard work to listen to because it was challenging some basic ideas I have carried with me and which have formed my world view. However many Skeptiko shows do that, we need to be challenged. I really want to believe there is more than just this physical existence in a world that appeals to me less and less due to the greed, inequality, sadness and injustice that I see. It reassures me that someone with your intellect, status and sciencific background who has spent a great deal of effort investigating yogic practices has come to the conclusions you have but on the other hand the human mind has an unlimited capacity for creating an internal world that fits with what we want to believe. Although I dislike it greatly, I cannot dispel the possibilty or ? probability that we are purely physical biological organisms, that being aware of our own mortality create complex illusionary paradigms to soften the knowledge that we will die and that will be the end of it.

Hi Doug, thank you, Sir, for your most kind reply. Yes, I can relate that having one's basic ideas challenged can be frustrating, just in general terms. Over time I have come to see the value of it, and so, as you can see on the board here, I am actively seeking out that people challenge my ideas. I think when it is done with respect and with a mutual understanding that we are all trying to become better people, that it can be a healthy and productive activity.

Yes, I agree. When one sees the state of the world, it begs for there to be something more. Materialism is a poor excuse for such things. Man has a moral nature and it breaks any normal person's heart to see our moral values so violated.

You raise an important point: one must always be wary of getting trapped in one's own delusions. I agree with that fully. That is part of why it is good to be out there and let people comment on and challenge one's ideas. It makes it hard to be self-deluded, as long as one listens when someone else criticizes, which I sincerely try to do, and it seems most people here on this message board also do. It is really great to find such a large group of people open to learning and growing in this fashion.

You raise a good point too about the possibility that we are just (as I like to say) "electric meat" and when we die, that is that. However, one of the things I say in the interview is something to the effect that the deepest mysteries are found in what appears to be the most common things. To me, the fact that we exist, that the universe exists, that there is existence at all, points to something very magical and special about existence. There is no way it can just be the random coming together of matter. People who say that lack imagination and do not see the deep inherent mystery of our existence. Something MUST lie beyond what we merely perceive with our senses. It might not be like anything we are sitting here saying with all these words. We might be completely off base in our speculations. But in speculating and trying to think about it, I do not think any of us here are wrong. I think people who believe that "what we see is all there is to see" are the ones who are wrong because they have been proven wrong time and time again. Think of Newton being replaced by Einstein. We do not see space bend, but now we know it does. Think of people who thought the Earth was flat. Think of people who thought disease was caused by evil spirits (as opposed to germs). I can give example after example of people who were wrong when they took existence merely at face value.

So, while I do not know with any great certainly what lies beyond, and I have a broader range of experience than most, I am wholly confident that there is more to all of this than meets the eye. Confidence in that conclusion is what keeps propelling me forward to keep learning and discovering on deeper and deeper levels about this completely mysterious thing we call "our existence".

Doug, thank you for the most stimulating conversation.

All my best,

Don
 
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.

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.

It just gives rise to an infinite regress of "why?" questions. I find it of interest that we can ask this infinite regress of questions and omit Darwinian evolution altogether and never miss it from the list. However, we cannot eliminate the ideas of dynamics, fluxes, flows, information, energy, all the terms used in physics.

If you ask the yogis: where do the gunas come from? They tell you the story of the Shiva-Shaki tattwa that I briefly explained in the last chapter of What Is Science? (the link says it as good as any thing). Where did the Shiva-Shakti tattwa come from? It just keeps repeating forever, some vast cycle completely beyond our intellectual comprehension. But at least the yogic claim to provide a method for discovering all this for oneself. There is no "I am the authority, you must believe what I say" in their teachings. Instead it is "here, here are the methods, go do it for yourself".

I know this is kind of incoherent, but I just got up...sorry if it seems that way....Best, Don.
 
I'd like to clarify something here. I mean on the face of it, the dynamics of non-equilibrium systems is a totally materialistic concept - which wouldn't really offer scope for the involvement of the non-material in any way.

However, systems close to chaos could obviously be controlled if an entity had a way to select a few critical quantum transitions - providing it was somehow possible for that entity to know what to do. Chaos magnifies tiny changes into macroscopic ones. One way it might know would be if it could see the consequences of multiple quantum choices for some distance into the future.

I have speculated that this is related to Dean Radin's presentiment. Does our non-physical self pick quantum eigenfunctions on the basis of knowledge of multiple possible futures?

I hope the above makes sense!

David

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. But what are the dynamics? Are dynamics made of matter? I would submit the answer is "no". Dynamics are expressed through matter, but somehow they transcend it too. 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. Or when we speak of "social dynamics", again it is immaterial. We are speaking of phenomena that are not made of atoms per se. The English language is not made of atoms of matter, although systems made of atoms (e.g. our bodies and brains) utilize this immaterial system.

Again, my point is that dynamics are mathematical patterns. So, these things are not materialistic at all. They are mental. Even the smarter materialists recognize this and are faced with the quandary: what is this "unreasonable effectiveness" of mathematics? Then you get absurd things from materialists, like Max Tegmark claiming the world is a mathematical object. This is a major weak point in the materialistic view of things. Math is not made of atoms of matter. If you want to attack the materialists, this is the place to do it.

Then, in what I consider a stroke of the greatest irony, you have the yogis who see the WHOLE universe as made of matter. To the yogi, our mind is material, the heavens and hells are material. Our soul is material. However, none of these are forms of physical matter, but different types of matter. This is the deep meaning of the word "gunas": they are the dynamical patterns found at all levels of relative being. The yogi does not preoccupying his or her self with mere physical matter. To the yogi, it is not "matter" vs. "not matter". The core distinction in yoga is "relative" vs "absolute". This is what physical matter, the mind, the soul, the spirit and the realms of the gods and demigods all have in common: they are relative things not absolute things.

So, in my opinion, yoga takes the whole discourse to a much higher level, one more befitting the majesty of our minds. The Western ideas of materialism are literally "down their in the mud" compared to how the yogis are using the mind and intellect.

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?
I'll stop here for now.

Best wishes, David.

Don
 
Wow! Newton debunked...cribbed his equation for gravitation from Kepler and Huygens, claimed the credit for Leibniz's calculus: "There was resistance against Newton in England, with a hard core of 20-25% of anti-Newton feeling within the Royal Society itself. How then did the current myth of Newton the scientist originate?"

Well worth a read.
that's gets to Tarpley's speculation about the merchants of Venice... simple answer money/power.
 
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